AbstractThe Bower's Berylmys (Berylmys bowersi) is one of the largest rodent species with a wide distribution range in southern China and the Indochinese Peninsula. The taxonomy and evolutionary history of theB. bowersiis still controversial and confusing. In this study, we used two mitochondrial (Cyt bandCOI) and three nuclear (GHR,IRBP, andRAG1) genes to estimate the phylogeny, divergence times, and biogeographic history ofB. bowersi. We also explored morphological variations among the specimens collected across China. Our phylogenetic analyses indicated that the traditionalB. bowersicontains at least two species:B. bowersiandB. latouchei.Berylmys latoucheiwas considered a junior synonym ofB. bowersidistributed in eastern China, which is confirmed to be distinguishable at specific level because of its larger size, relatively larger and whiter hind feet, and several cranial traits. The estimated split ofB. bowersiandB. latoucheiwas at the early Pleistocene (ca. 2.00 Mya), which might be the outcome of the combined effects of climate change in the early Pleistocene and isolation by the Minjiang River. Our results highlight the Wuyi Mountains in northern Fujian, China, as a glacial refugia during the Pleistocene and call for more intensive surveys and systematic revisions of small mammals in eastern China.