Abstract: In order to explore the sequence structure of fox Agouti gene and it’s mechanism to regulate the pelage color’s dividing. In this study, the major part of intron 2 sequence (1038 bp) of Agouti gene from the silver fox were obtained by PCR amplification and direct sequencing. This sequence was aligned with red fox, giant panda, horse, pig, goat, cattle, sheep, domestic cat and rabbit and the sequence similarities were 100, 85.82, 75.75, 73.31, 66.22, 65.98, 65.77, 60.45 and 58.82%, respectively. The result of the homology analysis showed that the genetic relationship between silver fox and red fox was the highest, which was consistent with that they belong to Vulpes of the Canidae animal in traditional classification. Based on the sequence of Agouti gene intron 2, the phylogenetic tree was constructed for silver fox and the other 9 species using Clustalx (1.83) software. The cluster result of phylogenetic tree of all species was basically consistent with the taxonomy of NCBI and was similar to the physiological characteristics of the species and their traditional classification. The above results provide the important biological information for researching the mechanism of the formation mechanism of the coat color and artificially improving the coat color quality of fox and so on.