There had been cultural contact between Nubians and Arabs long before the rise of Islam.
Islam spread to Sudan from the north, after the Islamic conquest of Egypt.
Nubia had already been Christianized, also from Egypt, hence the old Nubian church followed Coptic Christianity.
The Nubian Christian kingdoms of Nobatia, Makuria and Alodia fell to the Islamic invasions in 650, 1312 and 1504, respectively. From 1504, northern Sudan was ruled by the Muslim Funj Sultanate.
Southern Sudan, i.e. South Kordofan and what is now South Sudan, is part of Sub-Saharan Africa and was neither Christianized nor Islamized until the 19th century.
This region fell under Islamic rule under Muhammad Ali, and there has been religious and ethnic conflict ever since; the Mahdiyah uprisings (1881-1899) can even be seen as the origin of political Islamism and resulted in British control during 1899-1955.
Racial and religious conflicts between the Arab Muslim north and the Black African Christian South re-erupted in the First Sudanese Civil War (1955-1972), the Second Sudanese Civil War (1983-2005), the War in Darfur (2003-2010) and the ongoing conflict (since 2011).