The Funj were originally non-Muslims, but the aristocracy soon adopted Islam and, although they retained many traditional African customs, remained nominal Muslims. The conversion was largely the work of a handful of Islamic missionaries who came to the Sudan from the larger Muslim world. The great success of these missionaries, however, was not among the Funj themselves but among the Arabized Nubian population settled along the Nile. Among these villagers the missionaries instilled a deep devotion to Islam that appears to have been conspicuously absent among the nomadic Arabs who had first reached the Sudan after the collapse of the kingdom of Maqurrah. One early missionary was Ghulām Allāh ibn ʿĀʾid from Yemen, who settled at Dunqulah in the 14th century. He was followed in the 15th century by Ḥamad Abū Danana, who appears to have emphasized the way to God through mystical exercises rather than through the more orthodox interpretations of the Qurʾān taught by Ghulām Allāh.

The spread of Islam was advanced in the 16th century when the hegemony of the Funj enhanced security. In the 16th and 17th centuries, numerous schools of religious learning were founded along the White Nile, and the Shāyqiyyah confederacy was converted. Many of the more famous Sudanese missionaries who followed them were Sufi holy men, members of influential religious brotherhoods who sought the way to God through mystical contemplation. The Sufi brotherhoods played a vital role in linking the Sudan to the larger world of Islam beyond the Nile valley. Although the fervour of Sudanese Islam waned after 1700, the great reform movements that shook the Muslim world in the late 18th and early 19th centuries produced a revivalist spirit among the Sufi brotherhoods, giving rise to a new order, the Mīrghāniyyah or Khatmiyyah, later one of the strongest in the modern Sudan.

The “missionaries” were faqīhs (Islamic jurists) who attracted a following through their teachings and piety and laid the foundations for a long line of indigenous Sudanese holy men. They passed on the way to God taught them by their masters or founded their own religious schools or, if extraordinarily successful, gathered their own following into a religious order. The faqīhs played a vital role in educating their followers and helped place them in the highest positions of government, which allowed them to spread Islam and the influence of their respective brotherhoods. The faqīhs held a religious monopoly until the introduction, under Egyptian-Ottoman rule (see below), of an official hierarchy of jurists and scholars—the ʿulamāʾ, whose orthodox legalistic conception of Islam was as alien to the Sudanese as were their origins. This disparity between the mystical, traditional faqīhs (close to the Sudanese, if not of them) and the orthodox ʿulamāʾ (aloof, if not actually part of the government bureaucracy) created a rivalry that produced open hostility in times of trouble and sullen suspicion in times of peace. This schism has since diminished; the faqīhs continue their customary practices unmolested, while the Sudanese have acknowledged the position of the ʿulamāʾ in society.

Muḥammad ʿAlī and his successors

In July 1820 Muḥammad ʿAlī, viceroy of Egypt under the Ottoman Empire, sent an army under his son Ismāʿīl to conquer the Sudan. Muḥammad ʿAli was interested in the gold and slaves that the Sudan could provide and wished to control the vast hinterland south of Egypt. By 1821 the Funj and the sultan of Darfur had surrendered, and the Nilotic Sudan from Nubia to the Ethiopian foothills and from the Atbara River to Darfur became part of Muḥammad ʿAlī’s expanding empire.

The collection of taxes under Muḥammad ʿAlī’s regime amounted to virtual confiscation of gold, livestock, and slaves, and opposition to his rule became intense, eventually erupting into rebellion and the murder of Ismāʿīl and his bodyguard. But the rebels lacked leadership and coordination, and their revolt was brutally suppressed. A sullen hostility in the Sudanese was met by continued repression until the appointment of ʿAlī Khūrshīd Āghā as governor-general in 1826. His administration marked a new era in Egyptian-Sudanese relations. He reduced taxes and consulted the Sudanese through the respected Sudanese leader ʿAbd al-Qādir wad al-Zayn. Letters of amnesty were granted to fugitives. A more equitable system of taxation was implemented, and the support of the powerful class of holy men and sheikhs (tribal chiefs) for the administration was obtained by exempting them from taxation. But ʿAlī Khūrshīd was not content merely to restore the Sudan to its previous condition. Under his initiative, trade routes were protected and expanded, Khartoum was developed as the administrative capital, and a host of agricultural and technical improvements were undertaken. When he retired to Cairo in 1838, he left a prosperous and contented country behind him.

His successor, Aḥmad Pasha Abū Widān, continued his policies with but few exceptions and made it his primary concern to root out official corruption. Abū Widān dealt ruthlessly with offenders or those who sought to thwart his schemes to reorganize taxation. He was particularly fond of the army, which reaped the benefits of regular pay and tolerable conditions in return for bearing the brunt of the expansion and consolidation of Egyptian administration in Kassalā and among the Baqqārah Arabs of southern Kordofan. Muḥammad ʿAlī, suspecting Abū Widān of disloyalty, recalled him to Cairo in the autumn of 1843, but he died mysteriously, many believed of poison, before he left the Sudan.

During the next two decades the country stagnated because of ineffective government at Khartoum and vacillation by the viceroys at Cairo. If the successors of Abū Widān possessed administrative talent, they were seldom able to demonstrate it. No governor-general held office long enough to introduce his own plans, let alone carry on those of his predecessor. New schemes were never begun, and old projects were allowed to languish. Without direction the army and the bureaucracy became demoralized and indifferent, while the Sudanese became disgruntled with the government. In 1856 the viceroy Saʿīd Pasha visited the Sudan and, shocked by what he saw, contemplated abandoning it altogether. Instead, he abolished the office of governor-general and had each Sudanese province report directly to the viceregal authority in Cairo. This state of affairs persisted until Saʿīd’s death in 1863.

During these quiescent decades, however, two ominous developments began that presaged future problems. Reacting to pressure from the Western powers, particularly Great Britain, the governor-general of the Sudan was ordered to halt the slave trade. But not even the viceroy himself could overcome established custom with the stroke of a pen and the erection of a few police posts. If the restriction of the slave trade precipitated resistance among the Sudanese, the appointment of Christian officials to the administration and the expansion of the European Christian community in the Sudan caused open resentment. European merchants, mostly of Mediterranean origin, were either ignored or tolerated by the Sudanese and confined their contacts to compatriots within their own community and to the Turko-Egyptian officials whose manners and dress they frequently adopted. They became a powerful and influential group, whose lasting contribution to the Sudan was to take the lead in opening the White Nile and the southern Sudan to navigation and commerce after Muḥammad ʿAlī had abolished state trading monopolies in the Sudan in 1838 under pressure from the European powers.