Abstract: The yak heart fatty acidbinding protein (HFABP) gene was cloned and compared the nucleotide sequence of coding region with the homologous HFABP genes in other species including cow, sheep, goat, pig, human, rat, mouse, chick and zebrafish retrieved from the GenBank, and finally a phylogenetic tree was constructed by NJ, MP, ME methods using the coding region DNA sequences of the HFABP genes in all species. The results showed that the yak HFABP gene had 4 exons and 3 introns. The size of exon 1, exon2, exon3 and exon4 was 73,173,102 and 54 bp respectively; while the size of intron 1, intron2 and intron3 was 3 460,1 892 and 1 495 bp respectively.The size of CDS sequence of the yak HFABP gene was 402 bp which encoding 133 amino acids. The nucleotide sequences among different species were quite conservative. The homologies of the coding region of HFABP genes between the yak and cow, sheep, goat, pig, human, rat, mouse, chick and zebrafish were 998%, 978%, 970%, 928%, 888%, 833%, 831%, 764%, 687% respectively. The molecular phylogenetic tree among species was constructed according to the nucleotide sequence of the coding region of HFABP gene. The result indicated that the molecular phylogenetic tree had two branches, branch 1 contained Zebrafish, branch 2 contained yak and other species. Yak and cow, sheep and goat assembled separately, then assembled to a genus, and then assembled to a genus with pig and human, while the rat and mouse assembled to a genus, then assembled to a genus with human, and then chick. This result of phylogenetic clustering was identical to the zoological classification system, indicating that the HFABP gene was also fit to construct molecular phylogenetic tree among different species.