The people along the Nile river of the kingdoms and great powers have always fought against the the people of inland Sudan for centuries Since atleast the 17th century, central Govt.s have attempted to regulate and exploit the cattle herders of southern and inland Sudan.
When the British ran Sudan as a colony they administered the northern and southern provinces separately. he south was held to be more similar to the other eastern colonies-Kenya, Tangnyika, and Uganda = while northern Sudan was more similar to Arab-speaking Egypt.Northerners were prevented from holding any official powers in the south, and trade was discouraged between the two areas.
However, in 1946, the British gave in to northern presureto integrate the two areas. Arabic was made the language of administration in the south, and northerners began to hold positions in the south. The southern elites, trained in English, resented the change as they were kept out of their own govt. After decolonisation, most power was given to the northern elites based in Khartoum causing unrest to the south.
Secondly, The northerners are Muslim and follow Arab Muslim culture where as southerners are Christians having modern English education. In 1955, due to northern Muslim Arab domination rssulted in a mutiny among southern troops in Equatoria Province. These troops were upset that the Khartoum Govt. had failed to deliver on its promises to Britain that it would create a federal system.
Thirdly, In WWII the natural resources were supplied by the southerners, as ther are significant oil fields.Oilreenues make up at least 70 % of Sudan's export earnings. Moeover due to numerous tributaries of the Nile and heavier precipitation in southern Sudan, the south has also greater access to water and is ,therefore, much more fertile.The north is on the edge of the Sahara desert.A prallel war also raged between the Nuer and Dinka in the south.