Goitered gazelle (Gazella subgutturosa) is an important desert ungulate species and mainly lives in the desert and semi-desert of Eurasian areas. It was listed as a class II protected species in China. The International Union for Conservation of Nature and Natural Resources listed it as vulnerable (VU). In the spring 2010, many goitered gazelles were frozen, hungry and sick to death because of a snow disaster unlike any that happened in past 60 years at the Mt. Kalamaili Ungulate Nature Reserve. We sampled muscle tissue of 130 dead goitered gazelles when we participated in disaster relief in the field. The 102 cytochrome b (Cyt b) gene sequences of goitered gazelles were sequenced and analyzed. The results indicated a high haplotypic (H=0.855) and relatively low nucleotide diversity (π=0.00224) of Gazella subgutturosa at Mt. Kalamaili. Both haplotype network and phylogenetic tree based on the neighbour-joining and Maximum Likelihood methods showed two clades, suggesting a high degree of genetic differentiation. These two branches had undergone population expansion and sustainable growth. Combined with other 12 Gazella Cyt b entire sequences cited in GenBank , the phylogenetic trees of Gazella were reconstructed by neighbor-joining (NJ) and Maximum-likelihood (ML) methods, using Procapra przewalskii and Saiga tatarica as outgroups. The phylogenetic trees constructed by multiple methods (NJ and ML) proved that Gazella bennettii is the nearest species to Gazella subgutturosa. In addition, the divergence times between Gazella and Gazella subgutturosa were estimated as 1.08~2.5 million years ago(Mya) according to the Cyt b molecular clock.