According to previous studies, we found that HcTyp-1 gene may be involved in the formation of nacre color in shell of Hyriopsis cumingii. Primers were designed based on the cDNA sequence of HcTyp-1 gene in H. cumingii, and 8 SNPs were obtained by comparative screening and the correlation between SNPs and nacre colour-related traits was analyzed. Moreover, the location of HcTyp-1 gene on genetic map was studied. The study of the relationship between these polymorphic sites and shell nacre color traits found that, C+3057T showed a significant difference in the “a”; G+2985T and T+3006C had significant difference of L, b and a, dE respectively. Moreover, A+2834C, C+2919T and G+2986T all had significant difference in L, a and dE. Linkage disequilibrium analysis showed that there were 6 SNPs in high linkage disequilibrium except C+2912T and C+2983A. The result of haplotype analysis indicated that the frequency of T2 and T4 in the white mussels was significantly higher than that of purple group, but T6 and T8 were higher in purple group. The results suggested that the polymorphic loci in HcTyp-1 could be potential genetic markers for future molecular selection of different nacre color in H. cumingii. Furthermore, we mapped HcTyp-1 gene on LG16 of the previous linkage map, which will lay the foundation for the further study of the molecular mechanisms about this gene.