SignificanceState centralization occurs when previously separate communities are united, forming a single political system often associated with economy, trade, warfare, and culture. One example is the precolonial Kuba Kingdom of the Democratic Republic of the Congo (DRC). Using genetic data from over 690 individuals from the DRC, we compared individuals whose ancestors were part of the Kingdom to individuals from other neighboring groups. We found a genetic legacy of state formation that can be explained by the joining and subsequent mixing of groups at the time of state centralization, as well as evidence of gene flow facilitated by the Kingdom’s infrastructure. We characterize the genetic history of this region and show the power of DNA to reveal information on societal systems where few written records exist.