Three hundred and ninety accessions comprising 260 cultivated and 130 wild cowpea accessions were evaluated phenotypically using 27 cowpea descriptors. Morphological evaluation of some qualitative traits revealed 11.92% and 29.23% presence of pigmentation on the stem, 1.53% and 20.76% presence of stripes on the pod, and 0% and 20% presence of hairiness on the plant of cultivated and wild cowpeas respectively. As for the molecular analysis, sixteen SSR primers were employed for genotyping 48 accessions from both wild and cultivated cowpeas. The data generated a dendrogram with three clusters, two of which consisted of wild cowpea while the third cluster comprised all the cultivated cowpeas, including the yard-long-bean (Vigna unguiculata subsp. sesquipedalis) and Vigna unguiculata subsp. cylindrica accessions. Two wild accessions of subsp. dekindtiana, and one each of subsp. kgalagadensis and protracta clustered with cultivated cowpea indicating their relationships with cultivated cowpea, but not with other wild cowpeas. The numbers of polymorphic SSR bands in cultivated and wild cowpeas were 38 and 54, respectively, while the PIC values were 4.47 and 6.14, respectively, showing a greater genetic diversity in wild than in cultivated cowpeas. The subsp. dekindtiana had the highest number (80%) of shared SSR bands with cultivated cowpea followed by subsp. protracta with 54% of shared bands. Five species of wild cowpea have hairs and so could be used in breeding for resistance to insects.