Uganda and the Question of Southern Sudan: An Historical
Dr. S.K. Simba
Department of Political Science and Public Administration
A paper Presented at a Regional Symposium on Sudan’s
Neighbors and South Sudan Referendum on Self-Determination, 2-
3 October, Khartoum, organized by the Peace Research Institute
PRI-University of Khartoum & Society Study Centre (SSC)
The question of Southern Sudan refers to the long standing struggle for self determination
by Southern Sudan. The paper does not go into the causes and dynamics of these
struggles, however, it explores how these struggles have impacted on Uganda’s relations
with Sudan in general and Southern Sudan in particular. It covers the period between
1962, when Uganda got independence to the contemporary period of President Yoweri
Museveni. The main argument of the paper is that Uganda’s geographical proximity to
Sudan, the trans border ethnic communities between the two countries, ideological issues,
particularly the socialist doctrine external influences, particularly, Israelis interests and
US struggles against political Islam have been important factors in shaping Uganda’s
relations with Sudan in particular and Southern Sudan in general
Uganda has a long history of relationship with Southern Sudan, which go back to the pre-
colonial period. A good number of ethnic communities, notably the Kakwa, the Lugbara,
the Madi and Acholis, who find themselves at both side of the border are one people,
with a common history and cultural heritage. In addition to the cross border ethnic
communities, at one moment in history, Gondokoro, located in Southern Sudan was a
centre of activity for the European explorers, such as Sir Samuel Baker. The troops,
which Emin Pasha recruited in Southern Sudan in the middle 19th Century came to
constitute the first group of Uganda soldiers, the King African Rifles (KAR) until 1897
when they mutinied. Even when they mutinied they were not sent back to Sudan but
instead allocated land at Bombo in Uganda, where they have continued to play a very
positive role in Uganda social-political and economic history, particularly the military.
In 1914, the Order of State for the United Kingdom established the boundary between the
Anglo-Egyptian Sudan and Uganda. This Order delimited the Uganda Sudan border in
two sectors (1) from the Bahir al Jabal westwards to the Congo Nile watershed or
drainage area (2) from Lkae Rudolf to Bahir al Jabar.. Because of the transfer of Rudolf
Province from Uganda to Kenya, the Uganda-Sudan border was fixed in 1926 to the
current boundaries. Like most African states, it left several communities with common
histories and cultural heritage divided between two countries.
The crisis in Southern Sudan can be traced to the event which followed British war with
the Mahdi in the 19th Century. Following this war, the British policy over the Sudan had
to develop the three Southern provinces, that is Upper Nile, Bahr al Ghazel and the
Equatoria as distinct African provinces from the Islamic and Arab North. In 1945 as
African countries were in the formative days of their struggle for independence, it was
Britain’s proposal that Southern Sudan be made part of Uganda. However, by 1946 the
British had reversed its decision as a result of pressure from Khartoum for the
independence of the whole of Sudan. Britain also received pressure from Egypt in the
hope that an independent Sudan would be united with Egypt. This shift in policy was
concretized in the 1947. Subsequently Southern Sudan lost out being part of Uganda and
Uganda lost out in being in possession of Southern Sudan.
Post Independence Uganda the Question of Southern Sudan.
Uganda got its independence on the 9th of October 1962. Soon after independence the
Southern Sudan question became part of its post-colonial legacy. There were four major
factors, which influenced Uganda’s position towards Southern Sudan. The first factor
was Uganda’s geographical proximity to Southern Sudan. The second factor was religion.
The third factor was the cross border ethnic communities. The fourth factor was external
influence, particularly from Israel and the United States, which view Uganda as
strategically located in relations to their broader interests in the region.
Geographical Proximity: Uganda’s geographical position in relationship with
the Sudan makes it impossible for it to escape from the internal affairs of that
country. Even if it decided to remain neutral, internal strife in the Sudan will
make it the natural home for refuges and if these refugees are not properly
handled they can be a source of mutual suspicion between the two states.
Likewise, internal strife in Uganda, particularly the northern region will make
Sudan’s involvement/interest in Uganda’s internal affairs almost inevitable.
The Religious Factor: 70 per cent of the population of Uganda is Christian,
Specifically, the largest religious grouping in Uganda are Catholics, who
constitute about 45 per cent of the population of Uganda. The Catholic faith is
strong in Southern Sudan and in the context of state collapse in northern Uganda
and Southern Sudan the Catholic Church has been a very important provider of
social goods to the communities. In a struggle largely perceived as between Arab
Muslims and Christian, Ugandans are more likely to support the latter for equal
rights and the right for self determination
The Ethnic factor: When the final border between Uganda and the Sudan was
delimited in 1926, several ethnic groups were partitioned across the two countries.
These ethnic communities include the Kakwa, Madi, Lugbara Acholi. Toposa and
Didinga According to Ade Adefuye (1985) the presence of the Kakwa in the
Sudan was an important factor in that country’s internal politics. The Kakwa’s in
Uganda teamed up with their kinsmen in Southern Sudan to provide a common a
Black African Front against the Arab North. Secondly, these cross border
communities largely affected Uganda’s attitude towards the problem of Southern
Sudan. When Idi Amin, a Kakwa, came to power in Uganda, the political and
military support he received from Southern Sudan was the principal factor why he
remained in power for 8 years.
The Israel factor: The reasons for Israel’s interests in Uganda at the start of the
1960 were as the same as for Africa in general. Israel wanted to break through the
encirclement of the hostile Arab countries and open a way to a nearby continent,
and especially East Africa. Uganda’s special place came as part of the distant
memories of the Uganda Plan to settle Jews in 1918. Uganda is also important
because its long border with Southern Sudan, which according to Israel is was a
critical player in the politics of the Middle East. Specifically Israel strategy in the
1960 was to make it impossible for Sudan and Egypt to get united as some elite
were advocating and Uganda was strategically important in the struggle to defeat
the Sudan-Egyptian re-union. Uganda is also the source of the White Nile, on
which Egypt heavily depends. To control Egypt, one had to control Uganda.
In order to realize the above strategic objectives, several activities were carried out by
Israel in the 1960s, which affected Uganda’s relations with the Sudan in general and
Southern Sudan in particular. These activities, included among others, the following:
o Israel established a base in Northern Uganda and started training and
supporting Anya Nya troops, who also relied on Ethiopia as a sanctuary.
o To facilitate logistical support to the Anya Nya Guerrillas the Israel firm
Hiram Ze’eve built roads and an airfield in Arua
o It sent dozens of advisors to train Uganda infantry, paracuehutists, armed
corps, and the air force
o In the 1960, the International Arab media reported that Israel was building
its own air force in northern Uganda to enable attacking Sudan and Egpyt
if need arose.
o After the Six Day War of June 1967 Israel became a key financier of the
Anya Nya. It is believed that most of the weapons captured by Israel from
the Arabs during this war, were transferred to the Anya Nya guerrillas.
Obote’s Support for Southern Liberation movement and subsequent
Change of Policy:
Because of the factors mentioned above, from 1962 until 1969, Uganda’s support for
the liberation movement in Southern Sudan was an open secret. Probably the first
action by Obote was to try and unite the hitherto fragmented Southern resistance into
one strong force. Facilities for meetings of the various Sudanese political
organizations were provided by the Uganda government in the early 1960’s. The
objective was to come out with a common political front. In November 1964, the
Uganda government allowed the first General Convention of the Sudan to meet in
Kampala. At this meeting, Agree Jaden was elected President. In 1965, with Uganda
government support, most of these meetings were held in Southern Sudan.
Change of Policy
Between 1965 and 1969 Obote’s government vacillated between working towards the
peaceful settlement of the conflict in Southern Sudan and supporting blacks in
Southern Sudan. In 1969, particularly following the Nimiery coup in the Sudan,
Uganda policy towards the support of the Anya Nya guerrillas shifted towards
supporting the efforts of the government in Khartoum towards finding a lasting
political solution to the problem of Southern Sudan. Several reasons were
responsible for this change of policy and attitude
Rivalry between Amin and Obote: First, internally Obote was
worried of the growing influence of Amin in the Uganda army. Amin was
believed to be recruiting people from Southern Sudan into the Uganda army,
as he was building up his power base in Uganda.
Socialist wave on the African Continent: Between 1967 and 1970, a
wave of socialism was sweeping the African continent. Nimeiry came to
power with support from the Socialist fraternity in the Sudan. For some time,
until the attempted coup in 1972, Nimeiry expounded a socialist ideology. At
the same time Dr. Milton Obote announced a major ideological shift to the
left- the Common Man’s Charter, which it is alleged Nimeiry admired The
common ideological position the two countries were purporting to believe in
overshadowed other considerations, particularly ethnic and religious
The Buganda Question: in 1966, Obote had abolished kingdoms. This
was followed by an imposition of a republican constitution in 1967. These
moves resulted into demands for session by Buganda. Obote found himself in
a serious dilemma supporting movements towards self determination in
Southern Sudan and denying such demands in his own country.
Nimeiry’s Initiatives towards Southern Sudan: Caught up in the
dilemma mentioned above, when Nimiery promise to find a political solution
of the problem of Southern Sudan and after integrating several fighters of the
Anya Nya guerrilla movement into the government in Khartoum, Obote saw
no reason for the continued support of the guerrillas.
Unilateral Declaration of Independence (UDI). In 1968 Northern
Rhodesia under the leadership of Ian Smith, declared unilateral independence.
Even though the Commonwealth of Nations took a position to oppose the
UDI, Britain continued to offer military support both to Rhodesia and the
apartheid South Africa. This angered a number of African leaders, Obote
inclusive, creating a sense of mistrust between them and the Western World in
general. This mistrust was extended to Israel.
As a result of the above issues the Uganda government became particularly hostile,
especially Israel and its activities in the Southern Sudan.
And after the Six Day War, Uganda’s votes in the United Nations and other
International forum began to turn against Israel.
In 1969, General Zamir, Head of Israel Central Intelligence organization
sought refueling rights in Uganda in order to ferry arms to the Anya Nya
guerrillas. Obote, rejected this request, though Amin, the Commander in
Chief of the armed forces, worked with the Israelis to ensure that their
interests are taken care of.
In 1969, Rolf Steiner, a Western Germany mercenary who had been fighting
in Biafra, came to Uganda with the intentions of joining the Anya Nya
guerrillas. He was captured by the Uganda government and handed over to
the Sudanese government.
Angered by his change of policy, it strongly believed that Israel played an important role
in Obote’s overthrow in 1971. The only disappointing thing is that when Obote came to
seek refugee in the Sudan after his overthrow and when he tried to ask for military
assistance from the Sudanese government to try and regain power in Uganda, his requests
was denied. He had to re-locate to Tanzania.
Amin’s regime and the Southern Sudan Question:
In 1971 Amin took over power from Obote. He was caught up in a dilemma as far as the
question of Southern Sudan concerned. First, he was indebted to the Israelis who
allegedly helped him to take over power. Prior to the 1971, Amin had good relations with
Israel. He has taken a paratroopers course in Israel and the Israelis had given him a
name, Hagai Ne’eman, which means “a reliable helmsman”. He was particularly close to
Colonel Baruch Bar Lev. Secondly Amin was a Kakwa, one of the most important cross
border community. He was therefore indebted to his ethnic community, a number of
whom were actively involved in the struggles in Southern Sudan for self-governance. It is
believed that over 500 Anya Nya guerrillas participated in the 1971 military coup in
Uganda. Amin, therefore, shared Israelis interest in aiding the Southern rebellion.
The dilemma, however, was that Amin was a Muslim and as a Muslim he was expected
to support his Muslim brothers the world over, especially in their struggle against Israel.
For this, reason, Amin came under a lot of pressure from the Arab world, not only to
change his policy towards Israel but Southern Sudan as well. By 1972, Amin had
succumbed to this pressure. He made a significant change of policy, especially towards
Israel. Several other factors contributed to this change of policy.
Israel refusal to sell him weapons
Largely because he had purged the Uganda Army off the Acholi and Langi soldiers, who
by 1971 constituted 60% of the entire force, Amin was compelled to recruit former Anya
Nya guerrilla into the Uganda Army. A number of soldiers from the Anya Nya guerrilla
movement occupied very significant positions in Uganda’s military and political structure
through out Amin’s regime.
Post Amin’s Regimes and the Question of Southern Sudan:
In 1979 Amin is overthrown by a combination of Uganda exiles and the Tanzanian
People’s Defense Forces (TPDF). This overthrow had some implication on the Uganda
A number of former Amin’s soldiers, some with Sudanese ethnic links retreat into
Southern Sudan. They formed several rebel groups, the most significant of which
were, Uganda National Rescue Front (UNRF) and the West Nile Bank Front
Nimeiry, was particularly not happy with the new regime in Uganda. There was
hear that the former Anya Nya guerrilla, who had been successfully integrated
within the Uganda Army, would come back to constitute a military threat in
Southern Sudan. Secondly, a large number of Uganda refugees in Southern Sudan
following the overthrow of Amin, were seen as a security threat.
President Yoweri Museveni and the Southern Sudanese Question:
In 1981, Museveni launched a guerrilla war in Uganda. In 1983 a civil war in Southern
Sudan resumed under the leadership of John Garang. The two guerrilla leaders had two
things in common- they both studied at Dar es Salaam University at the same time and
they were very close friends. Secondly, they both at one time confessed to believe in
In spite of the closeness of the two rebel leaders there is no evidence that they had close
military cooperation in their guerrilla struggles between 1983 and 1986. This was
probably due logistical problems. Instead Museveni got military assistance from Libya,
which was more inclined to the Khartoum government than the SPLA.
In 1986, Museveni takes over power in Uganda. This significantly affected Uganda’s
relations with the Sudan. It also affected Uganda’s attitudes towards the question of
Southern Sudan in several ways.
First, the capture of power by the NRA, was seen as a bad example in the region.
For the first time a guerrilla movement has overthrown an independent African
government with minimal external support. This was an inspiration to other
guerrilla movements in the region, SPLA inclusive. Basically all neighboring
countries, except Tanzania became suspicious of the Kampala regime.
Second the defeated Uganda National Liberation Army retreated into Southern
Sudan. Numerous rebel groups were formed inside Sudan, the most important
one’s being the Uganda People’s Democratic Army/Movement, which had rear
bases in Southern Sudan. The UPDA, was, however, short lived. Following the
conclusion of a peace agreement with the Uganda government in 1988, it ceased
being a threat. Nevertheless, other rebel groups emerged notably the Lord
Resistance Army, which constituted a much more serious threat
Support for Each Others Rebel Groups
It is difficult to figure out who started supporting whose enemy. What is clear, whoever,
is that Uganda openly supported the Sudanese People’s Liberation Army/Movement and
the Sudanese government is alleged to support both the Lord Resistance Army and the
Allied Democratic Front.
Nature of support: Uganda’s Support for SPLA included the following activities
After the loss of loss of Ethiopia as its main base Uganda become very important
to the SPLA. According to the ICG, the Uganda People’s Defense Force first
provided clandestine support to the SPLA in the 1980s. The relationship quickly
evolved into open financial and military assistance as well as direct involvement
in operations alongside the SPLA1
Military cooperation includes monthly joint security meetings at a very senior
level. UPDF provides training for SPLA officers and advise to SPLA leadership.
A larger number of Uganda soldiers remain in South Sudan-particularly in
Western Equatoria and Western Bahr el Ghazal states, ostensibly to counter any
incursions or further passage of the LRA. SPLA dedicates four brigades in the
LRA hunt, including two combat ready reconnaissance companies that operate
along the Ugandans in the CAR.2
The CPA between the Southern rebels and the Sudanese government recognized
the SPLA as the official army of a semi-autonomous Southern Sudan. Uganda has
used this as an opportunity to offer military training to SPLA, particularly at its
prestigious college, the Senior Command and Staff College, Kimaka
Reasons for the Support: There are several reasons, why the Kampala
regime has continued to offer political, diplomatic and military support to the
SPLA. The reasons are strategic, personal, social and economic.
1. The Buffer Hypothesis: If Southern Sudan became independent, it would
make it difficult for Sudan to provoke or harm Uganda. An independent
Southern Sudan would be a buffer between Uganda and the Arab
countries. Uganda and Ethiopia together would constitute an African
barrier to the exclusive rule over the sources of the Nile
2. Personal friendship- as mentioned above, Garang and Museveni were
great friends. The friendship goes back to their delays at the University of
Dar es Salaam
3. Ideological- in the late 1980s both leaders shared a common ideological
position- socialism. It is important to note that President Museveni had a
significant ideological shift in the early 1990s towards liberalism. At the
end of his death John Garang could also be described more as a nationalist
than a Marxist. These latter ideological shifts, however, did not undermine
the friendship of the two leaders
4. Uganda as a frontline State against Political Islam: in the 1990s to date,
Uganda has positioned itself as a frontline state in the struggle against
Islamic Fundamentalism. For this reasons it perceives itself as the most
strategic ally of the Western World particularly the United States. For this
reason it has to fit into the United States interests and political strategies in
the region, including support for the SPLA.
5. Sudan’s perceived support for LRA and ADF and Uganda support for
SPLA resulted into strained relationship between the two countries. 1995
the Sudanese government bombed Uganda territory which prompted
President Museveni to break diplomatic relations and increase support for
SPLA3 In retaliation, the Khartoum gave weapons, funds, military
intelligence and training to the Lord Resistance Army. The LRA was also
used to fight Sudanese proxy war against the SPLA
The Referendum: Which way Uganda
Following the Comprehensive Peace Agreement (CPA) Southern Sudan is supposed
to hold a referendum in 2011. The referendum is to determine whether Southern
Sudan becomes independent or not. In spite of Uganda’s support to the SPLA,
government has not come with a clear position. The closest position government has
made is that it will go by the will of the people of Southern Sudan, irrespective of
how they will vote.
If the people of Southern Sudan vote to remain within the Greater Sudan, Uganda’s
major concern that Greater Sudan should put into place mechanisms of political,
economic and social inclusiveness so that the people of the South do not feel
excluded and marginalized. Anything short of this, war is likely to resume and
because of Uganda’s geographical location, it will be affected in one way or another.
In case the people of Southern Sudan go for self-determination, Uganda has a lot to gain.
These gains include the following:
Increased trade opportunities: Since the signing of the CPA, Uganda trade with
Southern Sudan has tripled. Southern Sudan is the largest importer of Uganda
products. In 2008, Ugandan goods worth $250 million were sold to Southern
Sudan, which is three times the volume before the signing of the CPA. This
excludes the informal trade. Uganda’s informal cross-border sales alone into
Southern Sudan reached more than $900 million in 2008, the Uganda Bureau of
Statistics said in a June 2009 report. This was twice the 2007 figure. Increaded
trade almost doubled the value of Uganda’s exports to the European Union. The
cross-border trade is being helped by the ongoing re- construction of the road
connecting Juba to Uganda and the rest of East Africa, Ndinyenka said. The 119-
mile stretch from the Ugandan border town of Nimule to Juba is being re-built by
the Louis Berger Group Inc. under a $201 million contract financed by the U.S.
Agency for International Development.
In addition, Ugandans are believed to be the largest group of foreign national
living in Southern Sudan. Several trade agreements have been signed between the
GoSS and Uganda. In addition, the Uganda Export Promotion Board organized an
Expo in Juba in February 2010, to show case Uganda goods and to cultivate links
between the business communities of the two countries. According to the ICG, the
GoSS has allocated land in Juba on which the Ugandans plan to build a $2million
Market for the sale of their goods.4
Improved Communication: There are plans to revamp the defunct regional
railway system and extend the railway from Gulu to Juba
Enlarged East African Community: Apart from the trade relationship between the
two countries, it is highly anticipated that and independent Southern Sudan will
join the East African Community. The GoSS Information Minister, Barnaba
Marial Benjamin, is quoted to have said that if Southern Sudan votes for
independence, it will try to join the EAC.
Another State on the Nile River: Obviously, an independent state will call for a
negotiation of the Nile River Treaties. It will weaken Egyptian and Sudanese
position vis a vis the Nile Waters
In spite of the above perceived gains, there are several concerns which go with Southern
Sudan struggle for self determination.
Uganda’s support for an independent South Sudan undermines its long standing
position as a Pan Africanist State, a state interested in the unity of the African
Continent. There is a fear that this will give a “bad” example to African states,
Uganda inclusive with minorities, which feel marginalization, and which,
therefore are demanding for self governance. Interesting enough the most vocal
group in Uganda advocating for the interests of SPLA is the Pan Africanism
Expected war out of the fear that Northern Sudan particularly with the support of
Egypt may an independent Southern Sudan. In the context of such a war,
Uganda’s direct involved cannot easily be ruled out.
Dinka Dominance: Southern Sudan is ethnically heterogeneous. Its success will
depend on how inclusive it is. In case one ethnic group appears to dominant the
possibility of a new civil war and demands for self governing rights by other
ethnic minorities is likely.
Loss of its strategic importance: In the last 20 years Uganda has positioned itself
as a frontline state in the struggle against Islamic fundamentalism. This frontline
status and therefore strategic importance is likely to be lost with an independent
Middle Nile Valley State: the current government in Uganda is dominated by
people from the South (Bantu). The Northern ethnic groups, who have ethnic
affinity with the people of Southern Sudan, feel they have been marginalized.
This will be a dilemma for an independent Southern Sudan. Will they side with
their old friends who helped them attain the war, or will the perceived
marginalization of their kinsmen result into new forms of solidarity, including the
demand for the recreation of the mystical Lado state, which is believed to have
incorporated ethnic groups of Northern Uganda and Southern Sudan
Trade battles: Whereas Uganda gave sanctuary to hundred of thousands of
Sudanese, there appears to be a feeling that Ugandan are taking over the local
markets in Southern Sudanese cities, including small retail business, which ought
to have been left in the hands of the indigenous Sudanese. Ugandans operate
small businesses, work as taxi drivers, construction workers, administrative and
service personnel, jobs, which the locals believe should be left to them.
Border Disputes: even before the referendum, Southern Sudan and Uganda have
been involved in numerous border disputes and territorial claims. The land
disputes between Uganda and Southern Sudan are of two types. First, the
Sudanese are claiming customary boundary from the Madi and Aringa people in
Uganda. The claims put Moyo Town Council, parts of Metu and Lefori sub-
counties in Moyo and Midigo in Yumbe districts of Southern Sudan. The
demanded land extends from Karido River in Sudan to Kelenderia, through Opiro,
behind Moyo Secondary School, to Ebikwa River, and Seleseleya to Leya from
the east This continues westwards to West Eria Hill, Lefori and down to Wano,
Sera Jale and Lobulele. Unless mechanisms are put in place to handle such
claims, these boundary disputes can be a source of serious tension between
Uganda and Southern Sudan.
Ade Adefuye (1985) The Kakwa of Uganda and the Sudan: Ethnic Factor in National
and International Politics
Arye Oded, Israreli-Uganda Relations in the Times of Amin
Department of State United States of America International Boundary Study No.104-
October 1, 1970, Sudan-Uganda Boundary (Office of the Geographer: Bureau of
Intelligence and Research)
Dustan Wai (1979) The Sudan:Domestic Politics and the Foreign Relations under
Nimiery (African Affairs, Vol. 78, Issue 312), pp297-317
International Crisis Group (2010) Sudan: Regional Perspectives on the Prospect of
Southern Independence (Africa Report, No, 159 6th May 2010
International Crisis Group (2002) God, Oil & Country: Changing the Logic of War in
Sudan (ICG Press)
Neu, Joyce (2002) Restoring Relations between Uganda and the Sudan: The Carter