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Rock shell (Thais clavigera), a common neogastropod snail, is not only an organism with important pharmaceutical values but also a favorable biological indicator useful for monitoring contamination of metals and tributyltin. However, its wild population has been overharvested and its natural habitat has been destroyed. Thus, establishment of conservation strategy of T. clavigera is urgently needed. To provide genetic information required for this purpose, we isolated fifteen novel polymorphic microsatellite loci of T. clavigera. The number of allele per locus varied from 3 to 17. The expected and observed heterozygosity ranged from 0.3439 to 0.9128 and 0.3333 to 0.8611, respectively. Three loci (TCA44, TCA117 and TCA134) showed significant deviations from Hardy–Weinberg equilibrium after Bonferroni corrections and no linkage disequilibrium was detected. We expect these loci could be further applied in population genetics studies, which could benefit the conservation of this species.