The study intended to investigate the phylogeography of mid-altitude species, Japalura brevipes, which is the endemic to Taiwan. I used mitochondrial cytochrome b sequences and morphological characters to investigate the phylogeography. The molecular results showed that there are 16 haplotypes. The length of partial cytochrome b sequences is 617 bp including 84 informative sites, and the mean genetic distance is 5.4%. In phylogenetic analyses, three major clades were found in the phylogenetic trees. Moreover, these clades (north, central-north and south) corresponded to the geographic distribution. Analysis of population genetic structure revealed significant differentiation among populations, and most of the haplotypes were restricted to the locally. The morphological analyses showed that there is no difference between sexes at 18 characters, with the exception of the axilla-groin length and dorsal-crest scales. The Principal Component Analysis and Canonical Discriminate Analysis using 16 morphological characters showed the different results. Principal Component Analysis failed to separate populations. However, Canonical Discriminate Analysis could discriminate the populations of Guanwu, Nanheng, Sihyuantkou and Wuling Farm from others. Phylogeography of J. brevipes belonged to category 1 defined by Avise (2000). I infer refuge effect and dispersal ability hypotheses to explain the genetic structure of J. brevipes.