This study was conducted to characterize Dioscorea spp. in Kenya using morphological and molecular characteristics. Data on 22 morphological traits were subjected to cluster analysis and multivariate analysis using principal component (PCA). The dendrogram of cluster analysis revealed three main groups: Species distribution based on PC-1 and PC-2 showed the distantly related species in each quarter; D. alata L. (1 st quarter), D. bulbifera L. (2 nd quarter), D. cayenensis Lam. (3 rd quarter) and D. minutiflora Engl. (4 th quarter). In molecular characterization, one sub-cluster grouped D. minutiflora Engl. and D. burkilliana J. Miege as one genetic group. However not all D. minutiflora Engl. species were in one specific cluster showing that there may be variation within the species. D. alata L. and D. bulbifera were seen to be potentially related because they shared a common origin. D. bulbifera L. and D. cayenensis Lam. genotypes clustered together, indicating that the species might be closely related. Generally, the rbcL marker demonstrated the phylogeny of Kenyan Dioscorea spp L. Comparison of morphological and molecular data analysis gave almost similar results. From the study, the phylogenetic relationships of Kenyan Dioscorea spp. were established and morphological and molecular characterization was efficient in establishing species relatedness among Dioscorea spp.