Otis tarda is listed as a first-rating protected bird in China, which has two subspecies, O. t. tarda and O. t. dybowskii. The genetic diversity and phylogenetic differences between the two Otis tarda subspecies were analyzed by the mtDNA control region method that on behalf of the maternal genetic character and the microsatellite method that on behalf of parental genetic character. The number of haplotype, Л, δ and К of O. t. tarda are higher than those of O. t. dybowskii among three sequences of mtDNA control region (CtrIaL/CtrIIoH、L438/H772 and LCR2a/HCR8), and significantly higher than the population in the northwest of Songliao Plain. The numbers of alleles, Ho and He of O. t. dybowskii are lower than those of O. t. tarda among three microsatellites (Otmic08, Otmic16 and Otmic26). Therefore, the genetic diversity of O. t. dybowskii is obviously lower than that of O. t. tarda. The two subspecies are located at two phylogenetic branches, which confirmed that the phylogenetic relationship between two subspecie.Moreover, O. t. tarda has much more phylogenetic branches than O.t. dybowskii.