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To evaluate the evolutionary significance of karyotypic characters in red-backed voles (Rodentia, Arvicolinae, genera Clethrionomys and Eothenomys) from northeastern Asia, we constructed phylogenetic trees based on intron 1 sequences (ca. 580 bp) of the X-linked gene G6pd. Phylogenetic trees, constructed using neighbor-joining and maximum-likelihood methods, revealed two major clades in red-backed voles corresponding to the glareolus- and the rufocanus-cytotypes defined by a reciprocal translocation between chromosomes 1 and 9 based on G-band patterns. If confirmed, two types of X chromosome, acrocentric X and subtelocentric X, which have often been claimed to be traits of evolutionary and taxonomic significance, should be considered as examples of homoplasy because they occur sporadically in members of both rufocanus- and glareolus-cytotypes in red-backed voles.