Objectives: To understand the genetic mechanism of Sweet potato(Ipomoea batatasL.)is a nutritious food crop.Enhancing the nutritional value of storage roots is important goal of sweet potato breeding programs aimed at developing improved varieties for direct consumption,processing,and industrial uses.However,developing improved lines of sweet potato is challenging due to the genetic complexity of this plant and the lack of genome information.Short sequence repeat(SSR)markers are powerful molecular tools for tracking important loci in crops and for molecular-based breeding strategies; however,few SSR markers and marker-trait associations have hitherto been identified in sweet potato.Methods: In this study,we identified SSRs by using a de novo assembly of publicly available ESTs and mRNAs in sweet potato,and designed primer pairs based on SSR-containing sequences.The assessment of anthocyanin content was carried out in three years for a population of sweet potato germplasms.We mapped primers in aforementioned population.Results: 17 SSR markers showed a high association(P<0.05)with the anthocyanin content in the storage root using association analysis.The SSR markers identified here can be used to select varieties with desired traits and to investigate the genetic mechanism underlying anthocyanin formation in the purple-fleshed roots of sweet potato by further evaluation of a subset of sweet potato genotypes with various characteristics.