Objective To complete sequence of mitochondrial ATPase8，ATPase6，COX3 of Mongolian Gerbil determined basing on the PCR products． The sequence was analysied in phylogenetic tree，nucleotide composition and genetic distance． Methods The primer was designed according to the published sequences． The PCR product were sequenced and determined． Combined with known ATPase8，ATPase6，COX3 sequence of other rodents nucleotide composition and genetic distance were analysed; phylogenetic tree was constructed by minimum-evolution ( ME) methods and UPGMA methods． Result The ATPase8，ATPase6，COX3 gene were cloned in Mongolian Gerbil，which have high homology with rat，mouse and hamster ( 76 ～ 98% ) ; it is higher genetic relationship with rat，mouse and hamster by phylogenetic analysis; the G content ( 6. 9% ，10. 7% ，15. 2% ) are similar with feature of mtDNA; the A + T content ( 68. 2% ，64. 1% ，59. 2% ) are similar with feature of mammalian genome． Conclusion The ATPase8，ATPase6，COX3， gene sequence of mongolian Gerbil was determined for the first time． We found that Mongolian Gerbil have close genetic relationship with rat，mouse and hamster in this research． This research is an important work for study on evolution，structure and function of the mongolian gerbil mitochondrion．