The Southern Sudanese opposition boycotted the recent elections in Sudan because of a lack of proper election safeguards. Sudanese dictator and war criminal Omar al-Bashir was easily reelected. He threatened that the boycott would jeopardize next year’s referendum on Southern Sudanese independence. The planned referendum was part of the deal negotiated by the United States under President George W. Bush that ended the two-decade-long civil war that claimed more than a million lives. The predominantly Arab Muslim Sudanese government in Khartoum had grossly violated the human rights of the Christian and animist Southern Sudanese.
In addition to human rights violations, Sudan has a history of sponsoring terrorism (e.g. it harbored Osama bin Laden in the 1990s). The Southern Sudanese independence referendum is significant to the war being waged against non-Muslims by militant Muslims, like the one held in East Timor a decade ago to which militant Muslims reacted violently, as they oppose giving up any territory to non-Muslims.
The civil war that was fought in Southern Sudan is separate from the current violence in Darfur, where the Arab Muslim government is complicit in the genocide against black Muslims being committed by Arab militia.