The Khedive of Egypt, Isma'il Pasha, was concerned over the growing power al-Zubayr, and established the province of Equatoria and planned to colonized the area. Isma'il hired the British explorer Samuel Baker in 1869 to govern the area, and supplied him with soldiers and generous financing, but Baker was unable to extend Egyptian power over the area.

To dispose of Al-Zubayr, Isma'il dispatched the mercenary leader Muhammed al-Bulalwi and promised him the governorship of Bahr el Ghazal, if he defeated al-Zubayr. Instead al-Zubayr routed the invaders and killed al-Bulalwi. In 1873 Isma'il thus agreed to appoint al-Zubayr as governor.

Isma'il was still threatened by al-Zubayr and his independent base of power. The British media was also filled with stories about al-Zubayr the "Slaver King." In 1874 Charles George Gordon was appointed governor of Equatoria. In 1877 al-Zubayr travelled to Cairo to ask for the governoship of Darfur as well, but was placed under house arrest by Is'mail. Gordon defeated al-Zubayr's son, ending the merchants' control of the region. Despite this, Gordon still failed to exert authority over any territory in the region beyond the lands immediately around his few forts.

In 1878, Gordon was replaced by Emin Pasha (Eduard Schnitzer). The Mahdist Revolt did not spread south to the non-Muslim region, but cut off the South Sudan from Egypt, leaving Emin Pasha isolated and without resources. He was rescued in a mission led by Henry Morton Stanley.

Equatoria ceased to exist as an Egyptian outpost in 1889. Important settlements in Equatoria included Lado, Gondokoro, Dufile and Wadelai. In 1947, British hopes to join the southern part of Sudan with Uganda were dashed by the Juba Conference, to unify northern and southern Sudan.

Shilluk
Alleged coup d'état attempt
Equatoria
Egyptian conquest under the Muhammad Ali Dynasty