"No to the genocide of the Nuba," proclaimed placards carried in the Khartoum protest by the indigenous group whose members live mostly as herders and farmers in the mountainous region.
Another sign read "the Nuba mountains are not Darfur" -- the western region where 300,000 were killed and more than two million displaced in a civil war from 2003 under then-dictator Omar al-Bashir.
"We are demonstrating to denounce the killings and the displacement of our people in Lagawa," one protester, Ahlam Ali, told AFP.
At least 19 people were killed in the city of Lagawa last month, according to the United Nations, in clashes between Nuba peoples and the Messiria Arab tribe.
"We are the indigenous people, so they want to force us to leave our lands," said another protester, Said Issa.
"They use the force of the state and its weapons, but we will not be silent."
Pro-democracy activists regularly accuse Sudan's military rulers of exacerbating the ethnic tensions.
This year, more than 600 people have been killed and over 210,000 displaced in inter-ethnic conflicts in Sudan, according to the UN.
The violence generally flares in disputes over access to scarce water and land in the arid and climate-stressed country where farming and livestock account for 30 percent of the economy and 43 percent of jobs.