The neritid species Clithon retropictum (Gastropoda), an oviparous snail, is distributed in freshwater and brackish water in southern Korea, south-east Japan, southern China and Taiwan. This species is listed as a class II endangered species in Korea because of its decreasing population size. It has led to an increase in the need for genetic information about this species. For this aim, in this study, we developed microsatellite markers for C. retropictum by using nextgeneration sequencing. A total of 185,972 sequences containing motifs with a minimum of five repeats motifs were identified from 3,392,119 reads. Of the 46 loci screened among 49 individuals, 36 were successfully amplified and 21 were polymorphic among 49 individuals, with 14 tri-nucleotide repeats and 7 tetra-nucleotide repeats. All loci exhibited relatively high genetic variability except one locus (CR08), with an average of 10.33 alleles per locus, and the mean observed and expected heterozygosities were 0.661 and 0.758, respectively. Our results demonstrated the utility of next-generation sequencing as a method for the rapid and cost-effective identification of microsatellites. These 21 newly developed microsatellite markers will be informative tools for investigating the genetic structure and diversity among populations of this endangered species and will help facilitate effective strategies for its conservation.