Using magnetic-bead enrichment and PCR screening method, we obtained 19 pairs of microsatellite primers from Tridacna crocea. Comparison between Qilianyu and Yongxing Island wild populations with these markers shows:the mean allele number and the effective allele number were 11.105, 11.895 and 6.274, 6.173 respectively; the values of average expected heterozygosity were 0.776 and 0.788; the mean PIC was 0.730 and 0.744; high genetic diversity was maintained in those wild populations. Four loci significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction in each population. In addition, the transferability of all polymorphic short sequence repeats (SSRs) was assessed in five closely-related species. The test resulted in 7 loci amplifying and 6 loci being polymorphic in T. squamos; 3 loci amplifying and 1 loci being polymorphic in T. derasa; 5 loci amplifying and 5 loci being polymorphic in T. noae; 9 loci amplifying and 8 loci being polymorphic in T. maxima; 2 loci amplifying and 2 loci being polymorphic in H. hippopus.