Archaeobotanical evidence suggests that the beginning of cultivation and emergence of domesticated sorghum was located in eastern Sudan during the fourth millennium BCE. Here, we used a genomic approach, together with archaeobotanical and ethnolinguistic data, to refine the spatial and temporal origin and the spread of cultivated sorghum in Africa. We built a probability map of the origin of sorghum domestication in Eastern Africa using genomic data and spatial Bayesian models. The origin was located in Eastern Sudan and Western Ethiopia, in perfect concordance with recent archaeobotanical evidence. Calibrated on archaeological remains, our genomic-based model suggests that the beginning of the expansion of sorghum agriculture took place around 4,600 years ago. Spread of sorghum cultivation led to a sorghum population structure fitting ethnolinguistic groups at different scales, suggesting that human social groups and sorghum populations co-diffused. Consequently, ethnolinguistic barriers and social preferences, as well as adaptation to specific climate zones, have contributed to structuring domesticated sorghum diversity during its diffusion.