San-like peoples were among the Uganda region's earliest inhabitants. Over the centuries, however, they were overcome by waves of migrants, beginning with the Cushitic speakers, who probably penetrated the area around 1000 BC . In the first millennium AD , Bantu-speaking peoples moved into the highland areas of East Africa, where they cultivated the banana as a food crop. After AD 1000, two other migrations filtered through the area: Nilotic-speaking Sudanic people and Luo speakers.
In the region south and west of the Nile, a number of polities formed, most of them strongly centralized. North and east of the Nile, political organization tended to be decentralized. In the south, the kingdom of Bunyoro was the most powerful and extensive, but in the 18th century the neighboring kingdom of Buganda began to challenge its supremacy. The two states were engaged in a critical power struggle when the British explorers John Hanning Speke and J. A. Grant reached Buganda in 1862. They had been preceded some years earlier by Arab ivory and slave traders. Other foreigners soon followed. Sir Samuel Baker entered Uganda from the north shortly after Speke's departure. Baker described a body of water, which he named Lake Albert. Baker returned to Uganda in 1872–73 as a representative of the Egyptian government, which was pursuing a policy of expansion up the Nile. The first Christian missionaries, members of the Church Missionary Society of Great Britain, came to Buganda in 1877. They were followed in 1879 by the Roman Catholic White Fathers.
The missionaries were welcomed by the kabaka (ruler) of Buganda, Mutesa I, who hoped to gain their support or the support of their countrymen against the Egyptian threat from the north. When the missionaries displayed no interest in military matters and the Egyptian danger was removed by the Mahdist rising in the Sudan in the early 1880s, Mutesa became less amenable. His son, Mwanga, who succeeded Mutesa on the latter's death in 1884, was even more hostile, fearing the influence exerted over his subjects by both the missionaries and the Arab traders. The kabaka, therefore, began to persecute the Bagandan adherents of Christianity and Islam. Both sets of converts joined forces to drive the kabaka from his country in 1888. A few weeks later, the Christians were expelled by the Muslims. Mwanga then appealed to the Christians for help, and they finally succeeded in restoring him to power early in 1890.
In 1888, the Imperial British East African Co. was granted a charter and authorized to administer the British sphere of East Africa. The Anglo-German agreement of 1890 officially outlined imperial spheres of influence in East Africa. By that agreement, what is now Uganda and Kenya were to be considered British spheres and Tanganyika a German sphere. In 1890, Capt. F. D. Lugard was sent to Buganda to establish the company's influence there. Lugard obtained Mwanga's agreement to a treaty that placed Buganda under the company's protection. Shortly afterward, however, lack of funds compelled the company to withdraw its representatives from Buganda.
In 1894, the kingdom of Buganda became a British protectorate, which was extended in 1896 to cover Bunyoro and most of what is now Uganda. In 1897, Mwanga led a revolt against British encroachments; he was quickly defeated and deposed. His infant son, Daudi Chwa, succeeded him, and a regency was established to govern Buganda under British supervision. Under the Uganda Agreement of 1900, Buganda was
ruled indirectly by the British, who in turn used the Baganda leadership as agents to extend British control indirectly throughout Uganda. The agreement confirmed the privileged position of Buganda in Uganda and of the traditional chiefs in Buganda. Subsequent treaties for indirect rule were concluded with the remaining kingdoms over a period of years.
Buganda's rebuff of British policies following World War II marked the beginning of a conflict over the place of Buganda within the future evolution of the territory. Kabaka Mutesa II was deposed in 1953 when he refused to force his chiefs to cooperate with the British. He was restored to power in 1955 under a compromise agreement.
It was only at the constitutional conference convened in London in October 1961 that a place was agreed for Buganda in a federal relationship to central government. It was also decided at this conference that Uganda should obtain independence on 9 October 1962. At a second constitutional conference in June 1962, Buganda agreed to scale down its demands over financial matters and ended its threats of secession from the central government. In August, a federal relationship with the kingdom of Ankole was agreed upon, and the agreement used as a model for dealing with the remaining two kingdoms, Bunyoro and Toro.
On 9 October 1963, an amendment to the constitution abolished the post of governor-general and replaced it with that of president. Sir Edward Mutesa (Kabaka Mutesa II of Buganda) became Uganda's first president. In February 1966, the 1962 constitution was suspended and the Prime Minister, Milton Obote, assumed all powers of government. Parliament formally abrogated the 1962 constitution on 15 April 1966 and adopted a new constitution, which created the post of president and commander-in-chief; Obote was elected to fill this position on the same day. Obote declared a state of emergency in Buganda following a clash between the police and dissident Baganda protesting the new constitution. On 24 May, Ugandan troops took control of the kabaka's palace, and the kabaka fled the country.
Further revisions to the constitution enacted in June 1967 abolished the federal relationship of Buganda and the other kingdoms, making Uganda a unitary state. Uganda became a republic with an executive president, who would be concurrently head of state and government.
Following a failed assassination attempt on Obote in December 1969, Parliament declared a state of emergency on 22 December. Ten opposition leaders were arrested and all opposition parties were banned.
On 25 January 1971, while Obote was out of the country, Maj. Gen. Idi Amin led a successful military coup. Obote was received by Tanzania as a political exile. The Second Republic of Uganda was proclaimed on 17 March 1971, with Amin as president. In September 1972, Ugandans who had followed Obote into exile in Tanzania staged an abortive invasion. They were immediately overpowered, but tensions between Uganda and Tanzania remained high.
The expulsion of Asian noncitizens from Uganda in August 1972 also caused international tension, especially with the UK. Expulsion of numerous British nationals in 1973 and the nationalization of UK-owned enterprises beginning in December 1972, further aggravated relations with the UK. An Israeli commando raid on Entebbe Airport on 3–4 July 1976, which freed 91 Israeli passengers and 12 crew members held captive by pro-Palestinian radicals in a hijacked aircraft, was a severe blow to the prestige of Amin, who was suspected of collusion with the hijackers (20 Ugandan troops were killed during the raid).
Under Amin, Uganda suffered a reign of terror that had claimed 50,000 to 300,000 lives by 1977, according to Amnesty International. The expulsion of the Asians took a heavy toll on trade and the economy. Agricultural and industrial production also fell, and educational and health facilities suffered from the loss of skilled personnel. The collapse in 1977, essentially because of political differences, of the 10-year-old East African Community (members—Kenya, Tanzania, and Uganda) also dealt a blow to Uganda's economy.
In late October 1978, Ugandan forces invaded Tanzanian territory, but Tanzanian forces, supported by anti-Amin rebels, struck back and by January 1979 had entered Ugandan territory. Kampala was taken on 11 April 1979, and all of Uganda was cleared of Amin's forces by the end of May; Amin fled first to Libya and later to Sa'udi Arabia. Yusuf K. Lule, an educator, formed a provisional government but was ousted on 20 June in favor of Godfrey Binaisa. On 13 May 1980, a military takeover ousted Binaisa and installed Paulo Muwanga. Parliamentary elections administered by Muwanga and other supporters of Obote, who returned from exile in Tanzania, were held on 10 December 1980. The election results, which opponents claimed were fraudulent, gave Obote's Uganda People's Congress (UPC) a clear majority, and he was sworn in as president on 15 December 1980. A period of reconstruction followed, and Tanzanian troops left in mid-1981. Security remained precarious, however. An undisciplined soldiery committed many outrages, and antigovernment guerrilla groups, especially the National Resistance Army (NRA), which was supported from abroad by Lule and Binaisa, remained active.
Obote's second term in office was marked by continued fighting between the army and guerrilla factions. As many as 100,000 people may have died as a result of massacres, starvation, hindrance of relief operations. International groups denounced the regime for human rights abuses. On 27 July 1985, Obote was overthrown in a military coup and Lt. Gen. Tito Okello, commander of the armed forces, was installed as president.
The NRA continued fighting, however, and on 26 January 1986 it occupied Kampala. Three days later, NRA leader Yoweri Museveni assumed the presidency. By April the National Resistance Movement (NRM) government was in control of most of the country, but armed supporters of the Obote, Amin, and Okello regimes remained active in northern and northeastern Uganda, as well as opposition from Karamojong separatists and prophetic religious movements, most notably the Holy Spirit rebels of Alice Lakwena in 1987.
After 1990, except for tiny groups of bandits, rebel military action was almost eliminated. However, Museveni resisted introducing a multi-party constitution advocating "no-party government" instead. In late August 1992, parliament formalized the ban on party politics which officials of the UPC and Democratic Party, DP (both abolished by Museveni in 1986) rejected at a press conference. Nonetheless, parties became more active, despite the ban and police action.
Although lauded by western countries as a new breed of African leader, and Uganda as a role model for African development, there was growing criticism of Museveni for his lack of democratic credentials by rejecting pluralism. In July 1993, parliament enacted Constituent Assembly Statute No. 6, the basis for nonparty elections to choose a constituent assembly, which would consider the draft constitution released in December 1992 by an appointed commission. In a secret ballot election on 28 March 1994, Ugandans elected 214 delegates to the 288-member assembly. Also included were 10 delegates appointed by the president, 56 representing interest groups, 8 representing 4 parties that had contested the 1980 election.
In addition, the government introduced constitutional changes allowing the Baganda to restore their monarchy purely for ceremonial purposes. Ronald Mutebi, son of the former king, was installed as Kabaka on 31 July 1993. The monarchies had been abolished in the 1967 constitution. A second king was restored and a third was rejected by government.
In October of 1995, the new constitution was finally enacted. It replaced the interim National Resistance Council with a permanent parliament, and made minor changes in executive power, but its most noticed element was the prohibition of political party activity for five years.
The first popular elections for president since independence were held on 9 May 1996. Museveni won with 74% of the vote, Paul Ssemogerere got 24%, and Muhammad Mayanja 2%. Nonparty parliamentary elections for the 276-member (214 elected, 62 nominated by special groups) house followed on 27 June 1999. The elections were peaceful and orderly, but election conditions, including restrictions on political party activities, resulted in flaws. Elections were held again in March 2001 with Museveni claiming victory with 69% of the vote to 28% for Kizza Besigye. The results were upheld despite objections by the opposition.
By June 2003, there was growing concern over the government's inability to build political consensus in the country and to maintain peace and security. In the north, the Lord's Resistance Army (LRA), a cult-like Christian rebel group operated from bases in southern Sudan, and in western Uganda, the Allied Democratic Forces (ADF) stepped up rebel attacks from the DRC. Other rebel groups included Rwanda Hutu rebels, Uganda National Rescue Front-II, and the Uganda National Front/Army. Members of these rebel groups have murdered, raped, kidnapped, tortured, and abducted children using them as combatants, sex and labor slaves. UNICEF estimates that the LRA and ADF have abducted over 4,900 men, women and children since 1987, most of whom remain missing.
Museveni has tried to end the fighting through diplomatic and military means. He reluctantly accepted an Amnesty Bill in January 2000, which provided for pardon to any rebels who surrendered their arms within 6 months. Three months later, no rebels had complied. A highly publicized all-out offensive in 2002 also failed to achieve its goals, and independent observers have accused government troops of killing innocent civilians including women and children.
Though a cease-fire with President Joseph Kabila of DRC was signed, and most Ugandan troops were withdrawn from Congolese territory in early 2003, fighting on the DRC side of the border continued into May 2003, and indeed intensified between the Hema and Lendu in the Bunia area as a result of Ugandan interference. Museveni's relations with his once stalwarth ally, Rwandan President Paul Kagame, have been strained since hostilities broke out between the troops of the two countries in Kisangani, DRC in 2001. Failure to end these conflicts has driven away foreign investment, tourism, and has diverted funds away from other ministries to defense, cancelling much of Uganda's economic and social progress. Additionally, public sector corruption has hurt economic growth. However, Uganda has been praised for lowering the national rate of HIV/AIDS infection from nearly 30% in 1993 to less than 12% in 1997.