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A new species of ponyfish in the genus Photoplagios is described from material collected in coastal waters of northeastern Madagascar. Photoplagios antongil, new species, is distinguished from congeners by the presence of a broad midlateral stripe and two darkly pigmented flank patches located ventral to the lateral midline, which are presumably translucent in life but darkly pigmented in preservative due to a concentration of melanophores. The new species is further distinguished from P. leuciscus, the only externally similar species occurring in the region, by the absence of a large translucent triangular patch on the flanks, a much shorter second dorsal-fin spine, a straight predorsal profile, pigmentation pattern on the upper flanks, absence of black pigment in the pectoral-fin axil, and exposed conical oral dentition in two distinct rows. A phylogeny for Photoplagios is provided based on the simultaneous analysis of anatomical features of the light-organ system and nucleotide characters. The taxonomic status of Equula lineolata Valenciennes, in Cuvier and Valenciennes, 1835 is discussed, and the species is herein concluded to be a nomen dubium of uncertain placement beyond the family level.