The mud crab Scylla paramamosain plays a significant role in fishery resources inChina. In this study, we developed 18 polymorphic microsatellite markers in this importantcrab by 5' anchored PCR technique. A total of 125 alleles were detected in a singlepopulation of 32 individuals of S. paramamosain. The number of alleles per locus rangedfrom five to nine, with the allele size ranging from 166 bp to 316 bp. The polymorphisminformation content (PIC), observed and expected heterozygosity ranged from 0.39 to 0.88,from 0.33 to 0.92 and from 0.42 to 0.86, respectively. Three loci (Scypa13, Scypa14 andScypa15) deviated significantly from Hardy-Weinberg equilibrium (HWE) after Bonferronicorrection (P<0.0028), and no linkage disequilibrium was found between loci pairs. Thesepolymorphic microsatellite markers will be useful for the study of population geneticstructure, construction of genetic linkage maps and mapping of economically quantitativetrait loci (QTL) in S. paramamosain.