Species identification and delimitation are critical for biodiversity conservation. Recent mitochondrial-based phylogenetic studies of the genus Paramesotriton, a group of small salamanders inhabiting mountain streams in southern China and northern Vietnam, suggest that its diversity may be underestimated. In this study, we confirm and characterize a new species, Paramesotriton wumengshanensis sp. nov., using morphological, mitochondrial NADH dehydrogenase subunit 2 (ND2), mitogenome, and genomic evidence. This new species can be distinguished from other Paramesotriton species by characteristics such as rough and large body warts, large eyes, the absence of vestigial gills and gill filaments in adults, and distinctive vomerine teeth. Statistical analysis of the morphological data further showed that the new species is significantly different from its close relatives. Phylogenetic reconstruction based on concatenated and coalescent approaches, using both mitochondrial DNA and nuclear single nucleotide polymorphisms (SNPs) generated by restriction site-associated DNA sequencing, revealed that the new species forms a distinct lineage within the genus Paramesotriton, exhibiting a minimum genetic distance of 0.63% in mitochondrial ND2 compared to congeners. The observed cytonuclear discordance and minor mitochondrial differences among species may stem from historical gene flow and/or incomplete lineage sorting, and future studies using genomic evidence are needed to investigate their respective contributions. Based on this discovery, we recommend that independent evidence, especially genomic evidence, be integrated into the classification of closely related species to avoid falling into the trap of mitochondrial introgression.