The species diversity of Taiwan Hynobius salamanders has long been debated. In this study, we analyzed morphological and molecular data from these taxonomically problematic salamanders. Our results show that, based on mitochondrial sequence data, there are five distinct clades of Taiwanese Hynobius. This result is consistent with morphologically-based analyses. Three of the clades have been described as distinct species, and our results corroborate their recognition, while the other two are described as new species in this paper. The first new species described is a moderately large, five-toed species. Coloration of dorsum is yellowish brown with irregular, black, short stripes and a gray ventral surface. This species is found in the northern Central and Syueshan Mountain Range at elevations above 3000 m, and has an average cytochrome b sequence divergence from other Taiwanese species ranging from 5.2% to 10.1%. The second new species described is small but robust, has a short tail and limbs, and has four-toes on each foot. Its dorsal color is dark brown with white spots and it has 11 costal grooves. This species is distributed in the northern and central part of the Syueshan Mountain Range. The average cytochrome b sequence divergence between this new species and other Taiwan species ranges from 9.8% to 11.1%.