In the present study, populations of small-sized smiliogastrin barbs with a thickened and serrated last simple dorsal-fin ray distributed in the Main Ethiopian Rift were analysed. An integrated approach combining genetic markers and a variety of morphological methods based on a wide set of characters, including osteology and sensory canals, proved to be very productive for taxonomy in this group of fishes. The results showed that EthiopianEnteromiusspecies with a serrated dorsal-fin ray are distant from the trueE. paludinosus(withE. longicaudaas a synonym) and the so-calledE. paludinosuscomplex involves several supposedly valid species with two distinct species occurring in the Main Ethiopian Rift area. A new species,Enteromius yardiensissp. nov., is described from the Afar Depression in the north-eastern part of the Northern Main Ethiopian Rift.Enteromius akakianusis resurrected as a valid species including populations from the Central Main Ethiopian Rift (basins of lakes Langano, Ziway, and Awasa). No genetic data were available forE. akakianusfrom its type locality.Enteromius yardiensissp. nov.is clearly distant fromE. akakianusfrom the Central Main Ethiopian Rift by CO1 and cytb barcodes: pairwise distances between the new species and the Ethiopian congeners were 5.4 % to 11.0 %. Morphologically, the new species most clearly differs from all examined Ethiopian congeners by three specialisations which are unique in the group: the absence of the anterior barbel, the absence of the medial branch of the supraorbital sensory canal, and few, 1–3, commonly two, scale rows between the lateral line and the anus.