A new species of the genus Protocobitis is described based on morphological comparisons and molecular analyses from specimens of a subterranean tributary of the Hongshui River, Lingyun County, Baise City, and a cave in Jinya Township, Fengshan County, Hechi City, Guangxi, China. Both morphological and molecular data support the validity of Protocobitis longibarbasp. nov. The new species can be distinguished from congeners by the following combination of characteristics: whole body except for head and area between pectoral-fin and pelvic-fin origin sparsely covered with minute scales; barbels elongate; five or six branched pectoral-fin rays and four branched pelvic-fin rays; vertebrae 4+42. Maximum-likelihood and Bayesian-inference phylogenetic trees exhibited congruent topological structures, exhibiting high node support for the monophyly of Protocobitis longibarba (BPP = 1; BS = 100), which was clustered with the other congeners.