The river sardine, Mesobola brevianalis (Boulenger, 1908), is the type species of Mesobola Howes, 1984. Standard phylogenetic analyses of partial sequences of the cytochrome oxidase I gene of individuals from populations across southern Africa that are currently identified as M. brevianalis showed that these populations represent four genetically distinct allopatric lineages. Furthermore, Engraulicypris sardella (Günther, 1868), the type species of Engraulicypris Günther, 1894, was convincingly nested amongst these clades. These findings support synonymisation of Engraulicypris and Mesobola syn. n.; restoration of Engraulicypris gariepinus (Barnard, 1943), stat. rev. for the lower Orange River population; description of two new species, Engraulicypris ngalala sp. n. and Engraulicypris howesi sp. n. from the Rovuma and Kunene river systems, respectively; affirmation of the synonymy of Engraulicypris brevianalis (Boulenger, 1908), comb. n. sensu stricto and Engraulicypris whitei van der Horst, 1934; and restoration of Engraulicypris bredoi Poll, 1945, stat. rev. and Engraulicypris spinifer Bailey & Matthes, 1971, stat. rev. from Mesobola. Discriminant function analysis of a truss network of five traditional morphometric measurements and 21 morphometric measurements that characterised the shape of the fishes was used to seek morphological markers for the genetically distinct populations. Only E. gariepinus was morphometrically distinctive, but live colouration differed between the lineages. Detailed taxonomic descriptions and an identification key for the species are provided. Keywords: Phylogeography, morphometrics, nomenclature, Mesobola, Engraulicypris, new species, new combinations, new synonym.