Forests of the Dahomey Gap are considered as refugia for many species. They play a crucial role in providing ecosystem services in an area devoid of forests. However, the impact of the way they are managed on the biodiversity they host has barely been investigated. Wild yams existing in these forests play a crucial role in maintaining the genetic diversity of cultivated yams. Indeed, studies of farmer practices have shown that, by way of ennoblement, wild yams collected and selected in the forests and old fallow areas are integrated into the cultivated pool. However, the genetic structure of wild yams is poorly understood. Using nine microsatellite loci, we investigated the population genetics of Dioscorea praehensilis in five forests in Benin, involving different management strategies and bioclimatic areas. Populations of D. praehensilis were strongly differentiated, consistent with an ancient separation of the forests. While the D. praehensilis population in a holly forest was undergoing mutation and drift equilibrium, the population collected from the most conserved forest was in a bottleneck. Moreover, in two forests with different management strategies, accessions from other forests were found, resulting from the displacement of yams following farmer migrations. No isolation by distance was detected, but a differentiation was found between populations of the Sudano-Guinean climate and the Guineo-Congolian climate. Our findings suggest differentiation due to forest isolations under past climatic conditions and more recent tuber flow through anthropogenic impacts.