The Sahelian region of Africa comprises the wild and domesticated range of pearl millet – Pennisetum glaucum (L.) R. Br., one of the most important cereals under production today. Cultivation in Africa runs primarily through the Sahelian zone that is characterized by dynamic weather patterns and climate change. Sahelian farmers have developed cultivation systems using native crops and local seed management to cope with the climatic instability and environmental heterogeneity of the region. This research investigates the biogeography and genetic diversity of the recognized subspecies of pearl millet. Sixty-seven accessions of pearl millet germplasm from thirteen African countries were analyzed using morphological and molecular methods. Thirty-two phenotypic and phenological traits were collected over two growing seasons to investigate differentiation and genetic variation of morphology across subspecies. These accessions were then evaluated at the genomic level using molecular markers. Fourteen simple sequence repeats (SSRs) were utilized to explore genetic structure and differentiation at the molecular level. Results from both studies indicate that pearl millet does not follow a standard pattern of genetic differentiation and reduction in genetic diversity as seen in other species that have undergone domestication. Morphological and molecular genetic diversity is extremely high in all types of germplasm analyzed with very little genetic structure or division among subspecies found at genetic and geographic levels. These results conclude that pearl millet in the Sahel is actually one large population or meta-population rather then three distinct subspecies. This is likely the result of introgressive hybridization that is a product of natural selection and farmers' management practices.