Total population size of the chiru (Pantholops hodgsonii), a species endemic to the Tibetan plateau, has undergone a severe decline in the past several decades. This study investigates the genetic variation, evolutionary history, and current population relationships among the 3 main populations of the chiru. Samples from Xinjiang, Xizang (Tibet), and Qinghai provinces in western China were collected and mitochondrial DNA control region sequences were analyzed. Overall nucleotide diversity (π) was 2.18% and thus indicated a relatively high genetic variation. Neutrality tests suggested a significant historical population expansion (Fu's Fs = −28.152), consistent with a population decline and observed pattern of mismatch distribution. Analysis of molecular variance suggested high degrees of gene flow among all the sampled populations, of which the Xinjiang and Xizang populations were revealed to be the most genetically related. It was inferred that calving ground might play a significant role in the course of gene exchange. These results shed light on the population history and current population status of the chiru, and have strong implications for the continued conservation of the species.