The Indo-Pacific marine atherinid fishes, Atherinomorus endrachtensis (Quoy and Gaimard, 1825) and Atherinomorus duodecimalis (Valenciennes in Cuvier and Valenciennes, 1835), having long been confused with each other, are redescribed as valid species based on the types and nontype specimens collected from the eastern Indian Ocean and West Pacific. Atherinomorus endrachtensis, known from the Philippines, Palau, North Sulawesi and Maluku Is. (Indonesia), and New Guinea, differs from other congeners in lacking a tubercle on the dentary and having the posterior tip of the upper jaw not extending beyond a vertical through the anterior margin of the pupil, usually 10–11 anal fin soft rays, 33–35 midlateral scales, a narrow midlateral band (ca. half midlateral scale width at anal fin origin), and 3 distinct longitudinal broken black lines laterally and ventrolaterally on the body. A lectotype is designated for Atherina lineata Gunther, 1872, regarded as a junior synonym of Atherinomorus endrachtensis. Atherinomorus duodecimalis, known from Sri Lanka, Thailand, Yaeyama Is. (Japan), the Philippines, Indonesia, New Guinea, Queensland (Australia), and New Caledonia, differs from other congeners in having a tubercle on the posterior end of the dentary, the posterior tip of the upper jaw not extending beyond a vertical through the anterior margin of the pupil, usually 12–13 anal fin soft rays, 35–38 midlateral scales, and a narrow midlateral band (ca. 1/2 or 3/4 midlateral scale width at anal fin origin). Atherina balabacensis Seale, 1910 is regarded as a junior synonym of Atherinomorus duodecimalis.