Abstract: Using the mitochondrial genomes of the muntjak (Cervidae:Muntiacus) sequenced by our lab.and 6 other species of Cetartiodactyla obtained from the GenBank,we calculated the sequence lengths and base compositions of their individual concatenated sequences of 13 amino acid sequences,13 protein-coding genes,2 rRNA genes,22 tRNA genes and control region.Sequence differences of protein-coding genes between cow/sheep,sheep/muntjak and muntjak/cow were analysed and genetic distances of the concatenated 12S rRNA and 16S rRNA genes among the 7 Cetartiodactyla species were calculated with MEGA.Based on the contatenated sequences of 13 inferred amino acid sequences of protein-coding genes,we constructed the phylogenetic tree with Neighbor-joining method,and discussed their phylogenetic relationships.Our results show:1)those species are divided into 3 clades which are a muntjak-sheep-cow clade,a pig-alpaca clade and a hippopotamus-whale clade;sheep and muntjak are first grouped into one branch and then cow is added to them;2)there is a closer relationship between muntjak and sheep than that betweeen muntjak and cow;3)the divergence between the muntjak and sheep lineages occurred at 14.7 million years ago and the one between the muntjak and cow lineages did at 16.0 million years ago.