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One the problems with fisheries assessment and management is the presence of multiple species in a single fishery. In such cases, each species may respond differently to management measures. In this study, we report for the first time the presence of a second species, the frigate tuna, Auxis thazard (Lacepede, 1800), in the fishery for bullet tuna, Auxis rochei (Risso, 1810), off the Iberian Peninsula and the western-central Mediterranean Sea. The bullet tuna is heavily targeted by both artisanal and commercial fisheries; thus, the presence of a second species may complicate management. Seven frigate tuna individuals (1.6%; 95% CI 0.7%-3.4%) were detected after analyzing more than 400 individuals, and they were unambiguously assigned to the species bullet tuna after the analysis of two unlinked genetic loci (nuclear gene Tmo-4c4 and the mitochondrial DNA control region). The unexpected presence of a species distributed in temperate and tropical waters, such as the frigate tuna in this northern location, may be a consequence of global warming. However, continuous monitoring with a validated methodology for species identification is needed to confirm this hypothesis.