The Sudan Liberation Army (SLA) elected Secretary-General Minni Arcua Minnawi as president, but the absence of President Abdel Wahed Mohamed el-Nur raised concern that infighting would erupt.
The elections were part of a congress, held in remote town and attended by up to 10,000 rebel supporters, aimed at ending differences that threaten to disrupt peace talks in a conflict that has killed tens of thousands in Sudan's remote west.
"Minni Arcua Minnawi won the elections for president with 486 votes," said congress spokesman Seifeddin Haroun. "There were five candidates but three pulled out."
Nur, who last week returned to rebel headquarters in Jabel Marra, central Darfur, for the first time in 18 months, said the elections would be invalid if he did not participate.
Nur was nominated but could not stand because he had broken election law by failing to present himself in writing, Haroun said.
A group of five mediators, shuttling between Jabel Marra and the congress site, had tried to stop the elections and prevent a split.
Suleiman Adam Jamous, the SLA's humanitarian coordinator, said he feared factionalism in the group would only help the rebels' government enemies.
"Any split will only serve the interests of the government," he said, adding that Nur would only likely take a few hundred fighters with him.
Differences among the SLA leadership have stalled peace talks in the Nigerian capital Abuja and escalated violence on the ground as local commanders vie for power.
Tens of thousands have been killed and more than 2 million forced from their homes during 2-1/2 years of revolt in the vast region. Non-Arab rebels took up arms in early 2003 accusing the Arab-dominated central government of monopolising wealth and power and neglecting arid Darfur.
Elections for the posts of secretary-general and vice president were under way, Haroun said.