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We report here the first case of natural hybridization between two yellowtails, Seriola quinqueradiata and Seriola lalandi, based on AFLP and mtDNA sequence data. Analysis of AFLP data using Bayesian model-based clustering methods revealed that 25 of 28 suspected hybrids are F1 hybrids and the remaining three are backcrosses to S. lalandi. Analysis of the mtDNA sequence indicated that hybridization is highly directional, as the majority of the F1 hybrids were offspring of S. quinqueradiata males and S. lalandi females. Considering the recent rapid distributional shift of S. quinqueradiata, our data indicate the need for further investigation of ongoing hybridization.