Pepper (Capsicum L.) is a widely consumed vegetable in South West Nigeria because of its nutritional and medicinal potentials. This study is aimed at evaluating genetic diversity among 30 pepper accessions collected from different pepper-growing areas in South West Nigeria using SSR markers. Amplification potentials and bands clarity were considered for selecting 17 among 29 SSR markers screened. Genetic diversity was evaluated using principal coordinates analysis (PCoA), cluster analysis (CA), and analysis of molecular variance (AMOVA). The sum of 208 alleles was detected with an average value of 12.24 alleles per locus for each accession. Genetic diversity was high in all loci with the mean value ranging from 0.23 to 0.77. The result of AMOVA showed that 2 % of the genetic diversity was due to interspecific variations while 98 % of the differences were due to intraspecific variations among accessions. The results of cluster analysis showed clearly high genetic similarity coefficient at > 71 %. The intraspecific and interspecific genetic relationships observed could be an integral part of the useful tools for genetic improvement of the genus Capsicum through breeding purposes especially the wild varieties.