Drylands of sub-Saharan Africa are highly threatened by climate and land-use changes. Species persistence is thus depending on genetic resources available in populations. One of the most important indigenous fruit tree species is baobab (Adansonia digitata L.) which is a significant species for food and nutrition security of local communities. The knowledge of intra-specific morphological variation is increasing while investigations on the genetic diversity of the tetraploid species are rare, especially in East African populations. In our study, we observed genetic and morphological variation patterns of baobab in Kenya to identify important gene pools and causes for the distribution of variation in this part of East Africa. In general, large genetic resources were found using microsatellite markers (SSR) which represent a geographical pattern. Thus, coastal and inland populations are genetically differentiated, whereas populations within regions cannot be separated. Morphological diversity patterns may reflect its habitat diversity and differ from genetics, while reasonable factors were not yet identified. However, both genetic and morphological variation patterns will be combined to identify gene pools especially adapted to several environmental conditions. Furthermore, the significance of humans for its distribution and diversity patterns will be discussed. Detailed knowledge of local gene pools of the valuable tree species is a prerequisite for conservation programs and the development of sustainable management strategies in the view of climate and environmental changes.