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Widespread polyphyly in stony corals (order Scleractinia) has prompted efforts to revise their systematics through approaches that integrate molecular and micromorphological evidence. To date, these approaches have not been comprehensively applied to the dominant genera in mesophotic coral ecosystems (MCEs) because several species in these genera occur primarily at depths that are poorly explored and from which sample collections are limited. This study is the first integrated morphological and molecular systematic analysis of the genera  Leptoseris  and  Pavona  to examine material both from shallow-water reefs (<30 m) and from mid- to lower-MCEs (>60 m). Skeletal and tissue samples were collected throughout the Hawaiian Archipelago between 2–127 m. A novel mitochondrial marker ( cox 1-1-rRNA intron) was sequenced for 70 colonies, and the micromorphologies of 94 skeletons, plus selected type material, were analyzed. The  cox 1-1-rRNA intron resolved 8 clades, yet  Leptoseris  and  Pavona  were polyphyletic. Skeletal micromorphology, especially costal ornamentation, showed strong correspondence and discrete differences between mitochondrial groups. One putative new  Leptoseris  species was identified and the global depth range of the genus  Pavona  was extended to 89 m, suggesting that the diversity of mesophotic scleractinians has been underestimated. Examination of species’ depth distributions revealed a pattern of depth zonation: Species common in shallow-water were absent or rare >40 m, whereas others occurred only >60 m. These patterns emphasize the importance of integrated systematic analyses and more comprehensive sampling by depth in assessing the connectivity and diversity of MCEs.

Polyphyly and hidden species among Hawaiʻi’s dominant mesophotic coral genera,LeptoserisandPavona(Scleractinia: Agariciidae)