Toxic (high phorbol esters) and nontoxic (low phorbol esters) jatropha accessions cannot be distinguished morphologically. Their seeds must be chemically analyzed through a complex and costly process using HPLC method. EST-SSR markers can be used to classify jatropha accessions with high and low phorbol esters. In this study, ninety-seven EST-SSR markers amplified the genomic DNA and showed polymorphism among 5 high phorbol esters accessions and 10 low phorbol esters accessions. These markers can be further exploited for jatropha improvement through marker-assisted breeding.