In order to study the correlation between HcTyr gene and shell nacre colour, genomic sequence fragments were amplified according to cDNA fragments of HcTyr gene. Regarding the detected SNP, the genotype and the polymorphic information (PIC) of 144 Hyriopsis cumingii were analyzed, and the correlation between SNP and shell nacre colour-related traits were further analyzed using Chi-square test. Moreover, the location of HcTyr gene on gene map was also studied. The results showed that 7 of the 8 detected SNP in HcTyr gene were significantly associated with shell nacre colour (L, a and dE). Haplotype analysis revealed that the frequency of three major predominant haplotypes (Ⅱ, Ⅲ, Ⅳ) in the white strain was significantly higher than that in the purple strain. And the other two major predominant haplotypes (Ⅴ and Ⅶ) showed significantly higher frequency in the purple strain. The haplotypes were further validated in commercial cultured populations and the results showed that Ⅳ and Ⅶ can be considered as predominant haplotypes for white strain and purple strain respectively. The results suggest that HcTyr could be candidate shell nacre colour related genes for H. cumingii, and some polymorphic loci in this gene could be potential genetic markers for molecular breeding. Furthermore, we mapped HcTyr gene on LG16 of the previous linkage map, which will lay the foundation for the further study of the molecular mechanisms about this gene.