Recent taxonomic and molecular work on the eagle rays (Family Myliobatidae) revealed a cryptic species in the northwest Pacific. This species is formally described as Aetobatus narutobiei sp. nov. and compared to its congeners. Aetobatus narutobiei is found in eastern Vietnam, Hong Kong, China, Korea and southern Japan. It was previously considered to be conspecific with Aetobatus flagellum, but these species differ in size, structure of the NADH2 and CO1 genes, some morphological and meristic characters and colouration. Aetobatus narutobiei is particularly abundant in Ariake Bay in southern Japan where it is considered a pest species that predates heavily on farmed bivalve stocks and is culled annually as part of a 'predator control' program. The discovery of A. narutobiei highlights the paucity of detailed taxonomic research on this group of rays. This discovery impacts on current conservation assessments of A. flagellum and these need to be revised based on the findings of this study.