Wild crop relatives are unique genetic resources for crop adaptation. Increasing pressure from agriculture threatens these populations both by reducing their habitats and by creating opportunities for wild-cultivated hybridization. In this study, we assessed the diversity of 38 wild pearl millet populations covering the whole known distribution of the species in Africa, which extends from Senegal to Sudan. Using genetic analyses of 10 cultivated varieties as control, we demonstrate the high diversity harbored by these wild populations. Diversity patterns suggest a diversity hot-spot in the southern part of the wild population’s range. However, this high wild genetic diversity could partly be explained by introgression from cultivated varieties. Such introgression is widespread in the Sahel. We validate the impact of cultivated introgression on the diversity of the wild population using a genetic introgression model. The introgression distorts the real assessment of the diversity of the wild population, and the burden of this gene flow compromises the long term survival of the wild populations’ original genome. Our study also questions the long term survival of the crop’s wild relatives.