Although Microphysogobio tungtingensis (Nichols, 1926) has been treated valid since it was described, its morphology remains vague, especially when comparing it with another similar species, M. elongatus (Yao & Yang, 1977). In this study, the types of both species were examined and also compared with several lots of specimens from a wide geographical range: there is no significant difference in morphology between them. Additionally, molecular evidence supported by mitochondrial gene sequence also showed low genetic distance in between. Thus, it is suggested that M. elongatus is a junior synonym of M. tungtingensis. While revising these two species, a new species, Microphysogobio punctatus sp. nov., was discovered that has a similar distribution with them both. However, it can be distinguished from its congeners by having a globular or oval shaped posterior air-bladder chamber which length 58.6%–82.8% of eye diameter; a narrow upper jaw cutting edge which less than half mouth width; a slender caudal peduncle with depth 34.6%–48.5% of length; and a six-branched-ray anal fin. This new species also has numerous small black spots on all fins which is also unique. The new species is morphologically and molecularly close to M. bicolor (Nichols, 1930).