The loach tribe Yunnanilini from China is reviewed using morphological characters and the complete mitochondrial genome of some selected species. Molecular data suggested that the tribe Yunnanilini is not monophyletic and divided into three clades. Species of the Y. nigromaculatus group form an independent genus and are placed in Eonemachilus. In the phylogenetic tree, Y. jinxiensis clustered with Paranemachilus genelepis, and Y. pulcherrimus clustered with Micronemacheilus cruciatus, indicating that Y. jinxiensis and Y. pulcherrimus belong to Paranemachilus and Micronemacheilus, respectively. Based on morphological data, four species from Guangxi, i.e., Y. bailianensis and Y. longibarbatus are placed in Heminoemacheilus, while Y. jinxiensis and Y. pulcherrimus, are placed in Paranemachilus, and in Micronemacheilus, respectively. Yunnanilus niulanensis and Y. qujinensis are treated as junior synonyms of Eonemachilus caohaiensis. The shared character of Eonemachilus, Micronemacheilus, and Yunnanilus is the short separation between the anterior and posterior nostrils. The genera can be distinguished from each other by mouth structure, characteristics of the lateral line and cephalic lateral-line canals, and papillae on the median part of both lips. The anterior and posterior nostrils of Heminoemacheilus and Paranemachilus are closely set. Characters distinguishing of Paranemachilus and Micronemacheilus are cheeks covered by scales and lips with papillae, respectively. Furthermore, our phylogenetic tree and morphological characters supported Traccatichthys as a valid genus, which can be distinguished from Micronemacheilus by anterior and posterior nostril closely set (vs. clearly separated). Four species are placed in Traccatichthys.