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Few phenomena have had as profound or long-lasting consequences in human history as the emergence of large-scale centralized states in the place of smaller scale and more local societies. This study examines a fundamental, and yet unexplored, consequence of state formation: its genetic legacy. We studied the genetic impact of state centralization during the formation of the eminent precolonial Kuba Kingdom of the Democratic Republic of the Congo (DRC) in the 17th century. We analyzed genome-wide data from over 690 individuals sampled from 27 different ethnic groups from the Kasai Central Province of the DRC. By comparing genetic patterns in the present-day Kuba, whose ancestors were part of the Kuba Kingdom, with those in neighboring non-Kuba groups, we show that the Kuba today are more genetically diverse and more similar to other groups in the region than expected, consistent with the historical unification of distinct subgroups during state centralization. We also found evidence of genetic mixing dating to the time of the Kingdom at its most prominent. Using this unique dataset, we characterize the genetic history of the Kasai Central Province and describe the historic late wave of migrations into the region that contributed to a Bantu-like ancestry component found across large parts of Africa today. Taken together, we show the power of genetics to evidence events of sociopolitical importance and highlight how DNA can be used to better understand the behaviors of both people and institutions in the past.

State 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.