In this study, 17 319 SSRs were identified from 221 037 ESTs of pepper using SSR finding soft. A total of 10 468 primer pairs were successfully designed and 1 538 primer pairs exhibited polymorphism by EPCR. Among the polymorphic primer-containing ESTs, 554 ESTs containing SSR motifs were matched onto the tomato genome, forming 12 linkage groups with an average of 45.75 makers per group. Analysis of GO (gene ontology) showed that 481 ESTs were classified mainly to be involved in primary metabolic process, cellular metabolic process and biosynthetic process. In the KEGG map, 91 ESTs were involved in 76 pathways (KEGG), 67 ESTs took part in metabolic pathways and 32 participated in biosynthesis of second metabolites.