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Mitochondrial DNA (mtDNA) control region (927 bp) and cytochrome b gene (1,140 bp) sequences of the Chinese water deer (Hydropotes inermis) from China and Korea were obtained to examine the taxonomic status of two subspecies, H. i. inermis from China and H. i. argyropus from Korea. Two sympatric mtDNA clades (a major clade from China and Korea and a minor clade from Korea) with an average genetic distance of 2.1% in the control region and 1.3% in the cytochrome b gene were detected. These findings are not consistent with the current classification by pelage color. We propose a reconsideration of the validity of the subspecies designation by the statistical comparison of morphological characters including body color. The major common mtDNA phylogroup in the two allopatric subspecies could be explained by the contiguous distribution of the Chinese water deer from east China to Korea until recent years. The restriction in the range and number of the Chinese subspecies after the last glacier might have caused the disappearance of the minor phylogroup in China. The taxonomic status of the two groups in Korea should be clarified using nuclear DNA marker analyses as well as morphological characters including pelage color.