The spotted eagle ray (Aetobatus narinari), a large coral reef-associated batoid of conservation concern, is currently described as a single, circumglobally distributed species. However, geographic differences in its morphology and parasite diversity have raised unconfirmed suspicions that A. narinari may constitute a species complex. We used 1570 bp of mitochondrial and nuclear sequence data (cytochrome b, cytochrome c oxidase subunit I, and internal transcribed spacer 2) to assess the validity of A. narinari as a single cosmopolitan species and infer its evolutionary history. Specimens from 4 major geographic regions were examined: the Central Atlantic, Eastern Pacific, Western Pacific, and Central Pacific. Phylogenies described 3 distinct, reciprocally monophyletic lineages with no genetic exchange among regions. Based on combined genealogical concordance and genetic distance criteria, we recommend that the Western/Central Pacific lineage be recognized as a distinct species from lineages in the Central Atlantic and Eastern Pacific. The latter 2 lineages, separated by the Isthmus of Panama, are proposed as subspecies. A basal position in phylogenetic analyses and statistical parsimony results support an Indo-West Pacific origin for the A. narinari species complex, with subsequent westerly dispersal around the southern tip of Africa into the Atlantic and then into the Eastern Pacific.