Despite the wide recognition of Homatula variegata (Dabry de Thiersant, 1874) as a valid Chinese loach, its type locality, identity and distribution still remain contentious. A molecular phylogenetic analysis based on the mitochondrial cytochrome b (cyt b) gene for samples from all known range of the species showed that three distinct species are involved. Morphological comparisons, coupled with examination on the types, confirmed that H. variegata s. str. is characterized by having a sparsely scaled predorsal body, an adipose crest along the dorsal midline of the caudal peduncle that extends forward to the vertical through the posterior end of the anal-fin base and a broadly rounded caudal fin. It is found merely in the Wei-He of the Huang-He basin. The Jinsha-Jiang population, previously misidentified as H. variegata, represents a distinct species, for which Homatula oxygnathra is the available name. Homatula laxiclathra, endemic to the Wei-He, is also a valid species distinct from H. variegata.