Venous blood samples from 50 unrelated Oroqen individuals living in Inner Mongolia were collected and their mtDNA HVR Ⅰ and HVR Ⅱ sequences were detected by using ABI PRISM377 sequencers. The number of polymorphic loci, haplotype, haplotype frequence, average nucleotide variability and other polymorphic parameters were calculated. Based on Oroqen mtDNA sequence data obtained in our experiments and published data, genetic distance between Oroqen ethnic group and other populations were computered by Nei’s measure. Phylogenetic tree was constructed by Neighbor Joining method. Comparing with Anderson sequence, 52 polymorphic loci in HVR Ⅰ and 24 loci in HVR Ⅱ were found in Oroqen mtDNA sequence, 38 and 27 haplotypes were defined herewith. Haplotype diversity and average nucleotide variability were 0.964±0.018 and 7.379 in HVRⅠ, 0.929±0.019 and 2.408 in HVR Ⅱ respectively. Fst and dA genetic distance between 12 populations were calculated based on HVR I sequence, and their relative coefficients were 0.993(P<0.01). A phylogenetic tree was constructed based on genetic distances and included Oroqen, Taiwan and South Han population in a clade, which indicated near genetic relation between them, and far relation with northern Han, Mongolian and other foreign populations. The genetic polymorphism of mtDNA HVRⅠ and HVR Ⅱ in Oroqen ethnic group has some specificities compared with that of other populations. These data provide a useful tool in forensic identification, population genetic study and other research fields.