A phylogeographic analysis of two bagrid catfi shes in Taiwan was conducted using sequence data from a portion of the mitochondrial DNA (mtDNA) control region. For Pseudobagrus brevianalis, which is most probably endemic to Taiwan, a total of eight haplotypes were detected in 189 specimens from nine river systems covering its entire distribution range, from northern to central western areas of the island. Obvious genetic differentiation was observed among its populations (average F ST = 0.753); in particular, the northernmost Tamsui River population was fi xed for a single endemic haplotype. Nested clade phylogeographic analysis (NCPA) indicated that the dispersal center of mtDNA was the area around the Touchien River and Holong River, north to the Miaoli Plateau, in northwestern Taiwan, suggesting both northward and southward dispersal in this species. There was no evidence for the validity of P. taiwanensis, the nominal species described from Taiwan, morphologically similar to P. brevianalis. We confi rmed that P. adiposalis was distributed discontinuously in three river systems; analysis of 42 specimens from the rivers indicated a total of four haplotypes and population differentiation (average F ST = 0.876). Fixation into a largely differentiated haplotype in the northernmost Tamsui River population was also found in this species, but different processes for this phylogeographic pattern were implied for the two species. Comparison with P. ussuriensis, a widespread continental species morphologically similar to P. adiposalis, suggested the possibility that P. adiposalis is a group of local populations of P. ussuriensis in Taiwan. Two migration routes vs. random fi xation scenarios for the population structure of P. adiposalis are discussed with information on other fi shes and the geological history of the island.