Identification of scombrids (tunas, mackerels, bonitos, etc.) is difficult when morphological characters are ambiguous or missing, such as with early life history stages or tissues found in the stomachs of predators. The mitochondrial cytochrome c oxidase subunit I (COI) gene region was evaluated as a molecular marker for the specific identification of the 17 members of the family Scombridae common to the western Atlantic Ocean. A 950 base pair region in the COI gene was sequenced from up to 20 individuals of each species, and suites of nucleotide polymorphisms that unambiguously distinguish among these scombrid species were identified. A shorter 250 base pair fragment of COI proved to be sufficient for species identification and was better suited for analyzing degraded tissue samples. Scombrid larvae collected in the Florida Straits and scombrid remains in the stomachs of large pelagic predators were used to demonstrate the utility of both the long and short COI fragments
