Eight accessions in pepper were analyzed with SRAP and SSR markers.Fifteen SRAP primers and eighteen SSR primers generated 321 and 109 fragments,respectively.The number of fragments per primer,the percentage of polymorphic loci was in turn 21.40,72.90% for SRAP markers,and 6.06,98.17% for SSR markers.Shannon’s information index (I),observed number of alleles (Na) and effective number of alleles (Ne) based on SSR markers were bigger than those based on SRAP.The results showed that SSR markers could detect more genetic diversity in the pepper accessions.The correlation analysis among genetic similarities based on SRAP and SSR data were significantly correlated.Both SRAP and SSR dendrograms could separate Capsicum frutescens accessions in China from the same species accession in American and C.annuum accession.