Sarcocheilichthys sciistius was originally described by Abbott in 1901. It was considered as a synonym of S. nigripinnis by later researchers. However, some recent studies suggested that S. nigripinnis from the Haihe River Basin and Yellow River Basin were different to S. nigripinnis distributed in southern China, and that these populations show a closer relationship with the Heilongjiang (Amur) River endemic species—S. czerskii and S. soldatovi. In this study, we examined one hundred and twenty-five specimens from nine sites of six river basins. Based on morphological and molecular systematic studies, we confirmed S. sciistius is a valid species, and S. czerskii, S. soldatovi were synonyms of S. sciistius. Sarcocheilichthys sciistius can be distinguished from S. nigripinnis by having more lateral-line scales (40–42 vs. 38–40), shorter lower lip and different pectoral and pelvic fins color. The phylogenetic trees reconstructed by Bayesian Inference and Maximum Likelihood based on the Cyt b gene also support S. sciistius as a distinct species.