Only one person survived the destruction of the village of Tarseen in the mountainous Jebel Marra area of the Darfur region, the Sudan Liberation Movement/Army said.
SLM/A, which has long controlled and governed an autonomous portion of Jebel Marra, appealed to the United Nations and international aid agencies to help collect the bodies of victims, including men, women and children.
"Tarseen, famed for its citrus production, has now been completely levelled to the ground," the group said in a statement on Tuesday.
"Nearby villagers are overwhelmed with fear that a similar fate might befall them if the ... torrential rainfall persists, which underscores the urgent need for a comprehensive evacuation plan and provision of emergency shelter," the group's leader, Abdelwahid Mohamed Nur, said in a separate appeal.
The SLM/A has remained neutral in the battle between the main enemies in Sudan's civil war, the Sudanese army and the paramilitary Rapid Support Forces.
The two foes are fighting over control of al-Fashir, nearby capital of North Darfur state, which is under siege from the RSF and has suffered famine.
Residents of al-Fashir and nearby areas have sought shelter in Jebel Marra, though food, shelter, and medical supplies are insufficient and hundreds of thousands have been exposed to the rains.
Tawila, where most have arrived, is in the throes of a cholera outbreak, as are other parts of Darfur.
The two-year civil war has left more than half of Sudan's population facing crisis levels of hunger and driven millions from their homes, leaving them especially exposed to Sudan's damaging yearly floods.
Sudan's army-controlled government expressed its condolences and willingness to assist.
The prime minister of a newly-installed RSF-controlled rival government, Mohamed Hassan al-Taishi, said he would be co-ordinating with the SLM/A on the delivery of aid supplies to the area.
