The coup removed political decision making from the control of the civilian politicians. Abbud created the Supreme Council of the Armed Forces to rule Sudan. This body contained officers affiliated with the Ansar and the Khatmiyyah. Abbud belonged to the Khatmiyyah, whereas Abd al Wahab was a member of the Ansar. Until Abd al Wahab's removal in March 1959, the Ansar were the stronger of the two groups in the government. 

The regime benefited during its first year in office from successful marketing of the cotton crop. Abbud also profited from the settlement of the Nile waters dispute with Egypt and the improvement of relations between the two countries. Under the military regime, the influence of the Ansar and the Khatmiyyah lessened. The strongest religious leader, Abd ar Rahman al Mahdi, died in early 1959. His son and successor, the elder Sadiq al Mahdi, failed to enjoy the respect accorded his father. When Sadiq died two years later, Ansar religious and political leadership divided between his brother, Imam Al Hadi al Mahdi, and his son, the younger Sadiq al Mahdi. 

Despite the Abbud regime's early successes, opposition elements remained powerful. In 1959 dissident military officers made three attempts to displace the Abbud government and to establish a "popular government." Although the courts sentenced the leaders of these attempted coups to life imprisonment, discontent in the military continued to hamper the government's performance. In particular, the Sudanese Communist Party (SCP), which supported the attempted coups, gained a reputation as an effective antigovernment organization. To compound its problems, the Abbud regime lacked dynamism and the ability to stabilize the country. Its failure to place capable civilian advisers in positions of authority, to launch a credible economic and social development program, and to gain the army's support created an atmosphere that encouraged political turbulence. 

Abbud's southern policy proved to be his undoing. The government suppressed expressions of religious and cultural differences and bolstered attempts to arabize society. In February 1964, for example, Abbud ordered the mass expulsion of foreign missionaries from the south. He then closed parliament to cut off outlets for southern complaints. Southern leaders had renewed in 1963 the armed struggle against the Sudanese government that had continued sporadically since 1955. The rebellion was spearheaded from 1963 by guerrilla forces known as the Anya Nya (the name of a poisonous concoction). 

Return to Civilian Rule, 1964-69

Recognizing its inability to quell growing southern discontent, the Abbud regime asked the civilian sector to submit proposals for a solution to the southern problem. However, criticism of government policy quickly went beyond the southern issue and included Abbud's handling of other problems, such as the economy and education. Government attempts to silence these protests, which were centered in the University of Khartoum, brought a reaction not only from teachers and students but also from Khartoum's civil servants and trade unionists. The so-called October Revolution of 1964 centered around a general strike that spread throughout the country. Strike leaders identified themselves as the National Front for Professionals. Along with some former politicians, they formed the leftist United National Front (UNF), which made contact with dissident army officers. 

After several days of rioting that resulted in many deaths, Abbud dissolved the government and the Supreme Council of the Armed Forces. UNF leaders and army commanders who planned the transition from military to civilian rule selected a nonpolitical senior civil servant, Sirr al Khatim al Khalifa, as prime minister to head a transitional government. 

The new civilian regime, which operated under the 1956 Transitional Constitution, tried to end political factionalism by establishing a coalition government. There was continued popular hostility to the reappearance of political parties, however, because of their divisiveness during the Abbud regime. Although the new government allowed all parties, including the SCP, to operate, only five of fifteen posts in Khatim's cabinet went to party politicians. The prime minister gave two positions to nonparty southerners and the remaining eight to members of the National Front for Professionals, which included several communists. 

Eventually two political parties emerged to represent the south. The Sudan African National Union (SANU), founded in 1963 and led by William Deng and Saturino Lahure, a Roman Catholic priest, operated among refugee groups and guerrilla forces. The Southern Front, a mass organization led by Stanislaus Payasama that had worked underground during the Abbud regime, functioned openly within the southern provinces. After the collapse of government-sponsored peace conferences in 1965, Deng's wing of SANU--known locally as SANU-William--and the Southern Front coalesced to take part in the parliamentary elections. SANU remained active in parliament for the next four years as a voice for southern regional autonomy within a unified state. Exiled SANU leaders balked at Deng's moderate approach and formed the Azania Liberation Front based in Kampala, Uganda. 
 
 

Anya Nya leaders remained aloof from political movements. The guerrillas were fragmented by ethnic and religious differences. Additionally, conflicts surfaced within Anya Nya between older leaders who had been in the bush since 1955, and younger, better educated men like Joseph Lagu, a former Sudanese army captain, who eventually became a strong guerrilla leader, largely because of his ability to get arms from Israel. 

The government scheduled national elections for March 1965 and announced that the new parliament's task would be to prepare a new constitution. The deteriorating southern security situation prevented elections from being conducted in that region, however, and the political parties split on the question of whether elections should be held in the north as scheduled or postponed until the whole country could vote. The PDP and SCP, both fearful of losing votes, wanted to postpone the elections, as did southern elements loyal to Khartoum. Their opposition forced the government to resign. The president of the reinstated Supreme Commission, who had replaced Abbud as chief of state, directed that the elections be held wherever possible. The PDP rejected this decision and boycotted the elections. 

The 1965 election results were inconclusive. Apart from a low voter turnout, there was a confusing overabundance of candidates on the ballots. As a result, few of those elected won a majority of the votes cast. The Umma captured 75 out of 158 parliamentary seats while its NUP ally took 52 of the remainder. The two parties formed a coalition cabinet in June headed by Umma leader Muhammad Ahmad Mahjub, whereas Azhari, the NUP leader, became the Supreme Commission's permanent president and chief of state. 
 
 

The Mahjub government had two goals: progress toward solving the southern problem and the removal of communists from positions of power. The army launched a major offensive to crush the rebellion and in the process augmented its reputation for brutality among the southerners. Many southerners reported government atrocities against civilians, especially at Juba and Waw. Sudanese army troops also burned churches and huts, closed schools, and destroyed crops and cattle. To achieve his second objective, Mahjub succeeded in having parliament approve a decree that abolished the SCP and deprived the eleven communists of their seats. 

In October 1965, the Umma-NUP coalition collapsed because of a disagreement over whether Mahjub, as prime minister, or Azhari, as president, should conduct Sudan's foreign relations. Mahjub continued in office for another eight months but resigned in July 1966 after a parliamentary vote of censure, which resulted in a split in the Umma. The traditional wing led by Mahjub, under the Imam Al Hadi al Mahjub's spiritual leadership, opposed the party's majority. The latter group professed loyalty to the imam's nephew, the younger Sadiq al Mahdi, who was the Umma's official leader and who rejected religious sectarianism. Sadiq became prime minister with backing from his own Umma wing and from NUP allies. 

The Sadiq al Mahdi government, supported by a sizable parliamentary majority, sought to reduce regional disparities by organizing economic development. Sadiq al Mahdi also planned to use his personal rapport with southern leaders to engineer a peace agreement with the insurgents. He proposed to replace the Supreme Commission with a president and a southern vice president and called for the approval of autonomy for the southern provinces. 

The educated elite and segments of the army opposed Sadiq al Mahdi because of his gradualist approach to Sudan's political, economic, and social problems. Leftist student organizations and the trade unions demanded the creation of a socialist state. Although these elements lacked widespread popular support, they represented an influential portion of educated public opinion. Their resentment of Sadiq increased when he refused to honor a Supreme Court ruling that overturned legislation banning the SCP and ousting communists elected to parliamentary seats. In December 1966, a coup attempt by communists and a small army unit against the government failed. The government subsequently arrested many communists and army personnel. 
 
 

In March 1967, the government held elections in thirty-six constituencies in pacified southern areas. The Sadiq al Mahdi wing of the Umma won fifteen seats, the federalist SANU ten, and the NUP five. Despite this apparent boost in his support, however, Sadiq's position in parliament had become tenuous because of concessions he promised to the south in order to bring an end to the civil war. The Umma traditionalist wing opposed Sadiq al Mahdi because of his support for constitutional guarantees of religious freedom and his refusal to declare Sudan an Islamic state. When the traditionalists and the NUP withdrew their support, his government fell. In May 1967, Mahjub became prime minister and head of a coalition government whose cabinet included members of his wing of the Umma, of the NUP, and of the PDP. In December 1967, the PDP and the NUP formed the Democratic Unionist Party (DUP) under Azhari's leadership. 

By early 1968, widening divisions in the Umma threatened the survival of the Mahjub government. Sadiq al Mahdi's wing held a majority in parliament and could thwart any government action. Mahjub therefore dissolved parliament. However, Sadiq refused to recognize the legitimacy of the prime minister's action. As a result, two governments functioned in Khartoum--one meeting in the parliament building and the other on its lawn--both of which claimed to represent the legislature's will. The army commander requested clarification from the Supreme Court regarding which of them had authority to issue orders. The court backed Mahjub's dissolution; the government scheduled new elections for April. 

Although the DUP won 101 of 218 seats, no single party controlled a parliamentary majority. Thirty-six seats went to the Umma traditionalists, thirty to the Sadiq wing, and twenty-five to the two southern parties--SANU and the Southern Front. The SCP secretary general, Abd al Khaliq Mahjub, also won a seat. In a major setback, Sadiq lost his own seat to a traditionalist rival. 

Because it lacked a majority, the DUP concluded an alliance with Umma traditionalists, who received the prime ministership for their leader, Muhammad Ahmad Mahjub, and four other cabinet posts. The coalition's program included plans for government reorganization, closer ties with the Arab world, and renewed economic development efforts, particularly in the southern provinces. The Muhammad Ahmad Mahjub government also accepted military, technical, and economic aid from the Soviet Union. Sadiq al Mahdi's wing of the Umma formed the small parliamentary opposition. When it refused to participate in efforts to complete the draft constitution, already ten years overdue, the government retaliated by closing the opposition's newspaper and clamping down on pro-Sadiq demonstrations in Khartoum. 

By late 1968, the two Umma wings agreed to support the Ansar chief Imam Al Hadi al Mahdi in the 1969 presidential election. At the same time, the DUP announced that Azhari also would seek the presidency. The communists and other leftists aligned themselves behind the presidential candidacy of former Chief Justice Babikr Awadallah, whom they viewed as an ally because he had ruled against the government when it attempted to outlaw the SCP.