Background: We investigated the polymorphisms of the bovine chemokine receptor-like 1(CMKLR1) gene. The coding region of CMKLR1 was screened in Qinchuan cattle by PCR-RFLP technology. Results: In this study, we discovered two single nucleotide polymorphisms (SNPs) (264G > C and 762C > T) in the coding region of the CMKLR1 gene. Hence, we described the BmgT120l and Pdm1 PCR-RFLP methods for detecting the 64G > C and 762C > T mutations, respectively. PCR-RFLP and sequencing were used to analyze the two loci of CMKLR1 gene in 324 individuals, which were randomly selected from breeding populations. Furthermore, meat quality traits in another 80 Qinchuan individuals were analyzed by the comparison between the genotypes and their phenotypic data. Conclusions: The results showed that the G264C SNP and C762T SNP of bovine CMKLR1 were significantly associated with backfat thickness (BFT) and water holding capacity (WHC), respectively.