Mollusks, used for analyses of genetic characteristics along the coast of Liaoning Province, are generally of enormous economic value. To study the genetic diversity and genetic differentiation of natural species, which remain unaffected by fishing and aquaculture, the trochid was used in this study. Along the coast of Liaoning Province, five populations of were sampled for the analyses of genomic SNPs and genetic characteristics using Genotyping-By-Sequencing (GBS). With a total of 1315987 SNPs detected, the observed heterozygosity values were calculated to be 0.0851-0.1161, which were generally less than the expected heterozygosity values (0.1424-0.1627), suggesting heterozygote deficiency and risk of population degradation. The loss of genetic diversity in the C4-ZH population may be due to the invasion of other species. Moderate genetic differentiation was found among the five populations. The C5-JZ population was found to have a higher genetic differentiation and lower gene flow. Three specific SNP markers were identified for the C5-JZ population. These results will contribute to the knowledge of the genetic characteristics of natural species along the coast of Liaoning Province and help to protect the coastal ecosystem.