Based on morphological and molecular analysis of Homatula species distributed in the Nanpanjiang River in Yunnan, China, we described a new species, Homatula robustasp. nov. It differs from its congeners by a combination of the following characters: naked and robust body with well-developed crests (caudal peduncle depth as a percentage of its length: 70.5–78.5%); lateral line complete; median notch on lower jaw; median gap on lower lip; three pairs of short barbels, with maxillary barbels extending posteriorly to anterior edge of eyes; branched dorsal-fin rays 8½; and vertebrae 37–39. It can further be distinguished from H. nanpanjiangensis by several differences of the caudal skeleton such as the number of hypural elements, the presence of epurale and the shape of neural and haemal spines. Phylogenetic analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene indicated that the new species represents an independent lineage. It is separated from other Homatula species by a minimum of 5.3% Kimura-2-parameter distance in the COI gene. Furthermore, we confirmed that Homatula wenshanensis should be a member of Homatula based on both skeleton and molecular evidence.