The yarkand hareLepus yarkandensis Günther, 1875 is one of the endemic mammals in China. We used mitochondrial control region (D-loop) sequences to investigate the genetic variation, population structure and phylogeography of the Yarkand hare from Xinjiang Uighur Autonomous Region. The Yarkand hare holds a high level of haplotype diversity in most populations. In contrast, we found a relatively low level of gene diversity in Niya and Shule populations. The pairwise mismatch distribution suggested a pattern of population expansion. Fu’s test of neutrality was significant for the total population (F s=−10.458), which also suggested a recent population expansion. The pattern of diversification among populations was not consistent with its geographic distributions. Significant divergence was found among some populations, however, no significant divergence among other populations. The results indicate some degree of dispersal of individuals may exist among populations in recent history. Due to past isolation and habitat fragmentation, genetic variation was reduced within populations and division among populations increased. In order to conserve genetic diversity of the Yarkand hare in isolated populations, in the future, it may be advisable to translocate individuals between isolated populations to maintain current levels of genetic variation.
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