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A new species of the butterflyfish genus Prognathodes (Chaetodontidae) is described from two specimens collected at a depth of 116 m off Ngemelis Island, Palau. Prognathodes geminus sp. n. is similar to P. basabei Pyle & Kosaki, 2016 from the Hawaiian archipelago, and P. guezei (Maugé & Bauchot, 1976) from the western Indian Ocean, but differs from these species in the number of soft dorsal-fin rays, size of head, body width, and body depth. There are also subtle differences in life color, and substantial differences in the mtDNA cytochrome oxidase I sequence (d ≈ 0.08). Although genetic comparisons with P. guezei are unavailable, it is expected that the genetic divergence between P. guezei and P. geminus will be even greater than that between P. geminus and P. basabei. It is named for the strikingly similar color pattern it shares with P. basabei.