Objective The relationship between the genetics polymorphism and phenotype of dog coat color was analyzed in order to give advice for the dog breeding. Methods The loci of R306ter in the canine MC1R gene were detected through the technology of PCR SSCP, and the relationships between the polymorphism of R306ter and coat color trait were analyzed. Furthermore, fragments with the polymorphism at R306ter were sequenced. Results\ By the method of PCR SSCP, the R306ter polymorphism was found with two alleles C and D and three genotypes CC, CD and DD. According to the results of sequencing of R306Ter, one terminal change from CGA to TGA at the position 306 was found. Conclusion\ According to the statistical analysis, no significant associations between the polymorphism of MC1R gene and the coat color were found and these results may be due to the differences of genetic background. For the variations of R306ter loci in MC1R gene, the polymorphism of PCR SSCP in the cross breed canine was detected.