The genetic composition of ancient Kigelia africana that is spread across Kenya has never been studied before. Kigelia africana a native forest species of Kenya as far as we know it. This tree is mostly found in the central, eastern, and northern coastal regions of the country where the Kikuyu, Akamba, and Taita tribes are the major inhabitants using it for making their traditional brew Muratina, Kaluvu, and Mbangara respectively. Unlike other tree species like Acacia, Kigelia africana genetic makeup has seldom been studied, even though a lot of evidence shows of its vast economic, cultural, and ecological value. Because of cultural practices, natural populations have been depleted from the wild. For this study, an investigation of four ancient tree populations will be done to explore and discover the genetic composition of Kigelia africana through DArTseq technology. Thirty-two (32) Plant seed samples will be obtained from various locations, their DNA extracted, libraries prepared and sequenced using the Illumina 2500 High Throughput sequencer. The data obtained will be analyzed to determine the genetic diversity, which will expose the population structure of the local species. The expected results should reveal genetic variation and differentiation among the local landraces and the improved cultivars. Measurement of variation will be based on an analysis of molecular variance (AMOVA) between and among populations, principal components analysis (PCA), and pairwise fixation index (Fst). Structure analysis and dendrogram construction will also be conducted. The results of this study will assist in helping decision makers, and conservators to make the necessary actions to conserve this culturally important tree.