Examination of the original descriptions and available type specimens of nominal species previously regarded as synonyms of Thrissina mystax (Bloch and Schneider, 1801), and many non‐type specimens representing an extensive geographic range, confirmed the validities of T. mystax, Thrissina porava (Bleeker, 1849), and Thrissina valenciennesi (Bleeker, 1866). Additionally, Engraulis poorawah Bleeker, 1872, a nominal species previously regarded as a junior synonym of T. mystax, is recognized as a junior synonym of Thrissina malabarica (Bloch, 1795). Diagnoses and detailed color descriptions are given for all of the valid species, in addition to clarification of their taxonomic histories, and neotype designation for T. porava. The phylogenetic relationships among 15 species of Thrissina (including T. porava and T. valenciennesi but not T. mystax) were reconstructed from the mitochondrial cytochrome oxidase I (COI) gene. T. porava and T. valenciennesi were not recovered as a monophyletic group, instead being divergent from each other and the other species of Thrissina by 12.4% and >11.7% mean uncorrected distances, respectively, confirming their reciprocal validity.