Taxonomic analysis of a group of morphologically similar and phylogenetically related ponyfishes (Perciformes: Leiognathidae) establishes the Equulites elongatus species group comprising three valid species: Equulites aethopos sp. nov., currently known only from southern Red Sea; Equulites elongatus (Gunther 1874), known from northern Australia, Indonesia and Myanmar; and Equulites popei (Whitley 1932), known from Japan, Philippines, Malaysia (Sabah), Thailand (Gulf of Thailand), Oman, the Red Sea, and Mozambique. Although E. popei has previously been regarded as a junior synonym of E. elongatus, the present mitochondrial DNA analysis revealed that these two nominal species are different and that they constitute a monophyletic group separate from other species of Equulites. The E. elongatus species group can be defined by the following of characters: slender body (20–30% in standard length), deeply incised posterior margin of the adipose eyelid, and ventral surface of breast completely scaly. Equulites aethopos sp. nov. differs from the other two species in having smaller eyes (eye diameter 53–68% of postorbital head length vs. 78–137%) and tips of neural and hemal spines of the fourth preural centrum distinctly expanding (vs. slightly expanding). Equulites elongatus is distinguished from E. popei by: scales above and below the lateral line 5–9 and 9–14, respectively (vs. 8–13 and 12–19), anus anteriorly located (distance from the pelvic-fin insertion to the center of anus 30–42% of the distance from the pelvic-fin insertion to the anal-fin origin vs. 35–50%), and more numerous dorsolateral dark marks (1–9 ring marks and 0–14 dark spots smaller than a half of pupil diameter vs. 0–2 and 0–5).