The evolutionary consequences of hybridization are poorly understood, especially in the marine realm where hybridization was once thought to be a rare occurrence. Previous research indicated that the lionfishes Pterois volitans and P. miles are sister species, both of which have been detected in the recent invasion of the Atlantic. Anecdotal data from the invasive range indicates they may hybridize, but previous studies have not examined the potential for these species to hybridize in the native range, or how such hybridization affects the distribution of genetic diversity. Here we address evolutionary divergence and population structure using mtDNA COI and two nuclear introns from 214 lionfish including four putative sister species (36 P. miles, 90 P. volitans, 32 P. lunulata, and 56 P. russelii) collected at 10 locations. Genetic data are supplemented with a re-examination of key morphological characters: dorsal, anal and pectoral fin ray counts. These data reveal two lineages (d = 0.041 in COI) among the four putative species: an Indian Ocean lineage, represented by P. miles and a Pacific Ocean lineage represented by P. lunulata and P. russelii. Lionfish identified as P. volitans appear to be hybrids between the sister linages of P. miles and P. lunulata/russelii, a conclusion supported by both the genetic data and morphology. The degree and geographic extent of introgression indicates widespread hybridization, or the absence of valid species distinctions between all four species. These findings also indicate that the lionfish invading tropical Atlantic Ocean, usually labeled P. volitans, is a hybrid.