The identification of interspecific hybrids represents an important issue for conservation biology and trade controls. In Italy, the commercial demand for sturgeon is rapidly increasing and interspecific hybrids represent a relevant part of aquacultural production. In this study we tested the suitability of the amplified fragment length polymorphism (AFLP) technique for sturgeon hybrid detection. Multilocus AFLP profiles were analysed by cluster analysis and assignment tests based on observed and simulated samples. Our results show that this approach can easily identify sturgeon hybrids, encouraging its application not only in sturgeon but also in other systematic groups.