At the same time that the Ottomans brought northern Nubia into their orbit, a new power, the Funj, had risen in southern Nubia and had supplanted the remnants of the old Christian kingdom of Alwa. In 1504 a Funj leader, Amara Dunqas, founded the Black Sultanate (As Saltana az Zarqa) at Sannar. The Black Sultanate eventually became the keystone of the Funj Empire. By the mid-sixteenth century, Sannar controlled Al Jazirah and commanded the allegiance of vassal states and tribal districts north to the third cataract and south to the rainforests.

The Funj state included a loose confederation of sultanates and dependent tribal chieftaincies drawn together under the suzerainty of Sannar's mek (sultan). As overlord, the mek received tribute, levied taxes, and called on his vassals to supply troops in time of war. Vassal states in turn relied on the mek to settle local disorders and to resolve internal disputes. The Funj stabilized the region and interposed a military bloc between the Arabs in the north, the Abyssinians in the east, and the non-Muslim blacks in the south.

The sultanate's economy depended on the role played by the Funj in the slave trade. Farming and herding also thrived in Al Jazirah and in the southern rainforests. Sannar apportioned tributary areas into tribal homelands (each one termed a dar pl., dur), where the mek granted the local population the right to use arable land. The diverse groups that inhabitated each dar eventually regarded themselves as units of tribes. Movement from one dar to another entailed a change in tribal identification. (Tribal distinctions in these areas in modern Sudan can be traced to this period.) The mek appointed a chieftain (nazir pl., nawazir) to govern each dar. Nawazir administered dur according to customary law, paid tribute to the mek, and collected taxes. The mek also derived income from crown lands set aside for his use in each dar.

At the peak of its power in the mid-seventeenth century, Sannar repulsed the northward advance of the Nilotic Shilluk people up the White Nile and compelled many of them to submit to Funj authority. After this victory, the mek Badi II Abu Duqn (1642-81) sought to centralize the government of the confederacy at Sannar. To implement this policy, Badi introduced a standing army of slave soldiers that would free Sannar from dependence on vassal sultans for military assistance and would provide the mek with the means to enforce his will. The move alienated the dynasty from the Funj warrior aristocracy, which in 1718 deposed the reigning mek and placed one of their own ranks on the throne of Sannar. The mid-eighteenth century witnessed another brief period of expansion when the Funj turned back an Abyssinian invasion, defeated the Fur, and took control of much of Kurdufan. But civil war and the demands of defending the sultanate had overextended the warrior society's resources and sapped its strength.

Another reason for Sann2ff nnar's decline may have been the growing influence of its hereditary viziers (chancellors), chiefs of a non-Funj tributary tribe who managed court affairs. In 1761 the vizier Muhammad Abu al Kaylak, who had led the Funj army in wars, carried out a palace coup, relegating the sultan to a figurehead role. Sannar's hold over its vassals diminished, and by the early nineteenth century more remote areas ceased to recognize even the nominal authority of the mek.

Data as of June 1991