Abstract: 【Objective】To clarify the correlation between the polymorphism of cation-dependent mannose-6-phosphate receptor（CD-MPR）gene（PmCD-MPR）and the low temperature tolerance of Pinctada fucata martensii，and to provide theoretical basis for the breeding of low temperature resistant strains of P. fucata martensii.【Method】The fulllength sequence of PmCD-MPR gene was cloned by rapid-amplification of cDNA ends（RACE），and real-time fluorescence quantitative PCR was used to detect the expression pattern of PmCD-MPR gene in various tissues of P. fucata martensii and under low temperature stress；based on the whole genome resequencing data of P. fucata martensii low temperature resistant line（R group）and Beibu Gulf wild population（W group），we screened for the single nucleotide polymorphism（SNP）loci in exon regions of the PmCD-MPR gene，and obtained the SNP loci related to the low temperature stress process of P. fucata martensii through the analysis of genetic polymorphisms，haplotypes，and the frequency calculations.【Result】The PmCD-MPR gene sequence was 902 bp in length，with an open reading frame（ORF）of 792 bp， encoding a total of 263 amino acid residues；the molecular weight of the protein encoded by the PmCD-MPR gene was 30.22 kD，and the theoretical isoelectric point（pI）was 5.79，which belonged to the hydrophilic proteins，and it contained a typical mannose-6-phosphate receptor（Man-6-P_recep）structural domain at amino acids 18-263. CD-MPR amino acid sequences were less similar at the N-terminal end and more similar at the C-terminal end；the phylogenetic tree constructed on the basis of CD-MPR amino acid similarity showed that P. fucata martensii was clustered with mollusks such as Crassostrea gigas and Aplysia californica，which was in line with the classical zoogeographic classification. The relative expression of PmCD-MPR gene was the highest in the hepatopancreas and significantly higher than that in the gonads，adductor muscle and mantle（P＜0.05，the same below）；the relative expression of PmCD-MPR gene in the gill tissues of P. fucata martensii in the low temperature stress group showed a tendency to increase first and then decrease with the prolongation of the stress time. A total of 34 SNPs were screened from the exon region of PmCD-MPR gene，and these 34 SNPs constituted 5 haplotype blocks and 15 haplotypes. Among them，the distribution frequency of GCC，TG and CCCTCT haplotypes in R population was significantly higher than that in W population，which was significantly correlated with the low temperature tolerance of P. fucata martensii.【Conclusion】The PmCD-MPR gene is involved in the low temperature response process of P. fucata martensii，and the genotypes and haplotypes that are significantly associated with low temperature tolerance traits can be used as candidate molecular markers for assisted breeding of low temperature tolerant lines of P. fucata martensii.