Seventy-eight cowpea accessions were studied using short sequence repeats (SSR) technique. Genetic structure of these accessions was studied using three SSR polymorphic primers, SSR-6206, SSR-6218 and SSR-6219. A total of eight loci were scored for the three primers with a total of ten alleles. Bayesian clustering method grouped the cowpea genotypes into 4 sub-populations. Ancestral allele frequencies ranged between 0.128 and 0.802, while allele frequencies within sub-populations ranged from 0.001 and 0.997. Allele frequency divergence among sub-populations ranged from 0.145 to 0.406. Expected heterozygosity between individuals in the same sub-population ranged from 0.084 and 0.26, Mean genetic differentiation among sub-populations ranged from 0.374 and 0.687, with a mean geneflow ranging from 0.228 and 0.837. There was relative uniformity within the sub-populations which can be accounted for by independent random genetic drift
