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Tufted deer(Elaphodus cephalophu)is a native of central and southwest China.It has been categorized as “Near Threatened”(NT)by the International Union for Conservation of Nature(IUCN).In this population genetic analysis,we explored the genetic diversity,structure and demography using mitochondrial DNA(mtDNA)control region(CR)sequence and 13 polymorphic microsatellite loci in two adjacent tufted deer populations(Wulingshan and Dabashan),living by the Yangtze River.Results suggest the presence of large genetic diversity in these populations.