Abstract: 30 microsatellite loci of Mereteix meretrix were developed using microsatellite -enhanced genomic library and expressed sequence tags ( ESTs ) . Genetic diversity was analyzed in a population consisting of 30 Individuals . 8 G-SSRs and 22 EST-SSRs were found to be polymorphic. In these 30 microsatellite loci , a total of 140 alleles were identified , the number of alleles varied from 3 to 6 , with a mean of 4.67 alleles per locus. Polymorphic information content ( PIC ) ranged from 0.172 to 0.744 . The observed heterozygosity ( Ho ) was from 0.040 to 0.720 , while the expected heterozygosity ( He ) was from 0.187 to 0.793 . The mean values of number of alleles , PIC , Ho , and He of G-SSRs were higher than those of the EST-SSRs . 24 of the 30 loci deviated from the Hardy-Weinberg equilibrium after Bonferroni correction . 11 EST-SSR identified from annotated genes were expected to be useful for mapping these genes in linkage maps . Interspecific transferability of the 30 markers revealed that 12 and 9 were polymorphic in M. lamarckii and M. lyrata , respectively. These loci obtained will lay a foundation for the study of genetic diversity , germplasm resources evaluation , marker-assisted selection ( MAS ) and other relevant research in M. meretrix , and these novel polymorphic SSR markers can be used for comparative mapping, gene tagging and QTL mapping among M. meretrix, M. lamarckii and M. Lyrata.