Random amplified polymorphic DNA (RAPD) analysis was investigated as an alternative to conventional electrophoresis for subspecies identification of largemouth bassMicropterus salmoides.Seventeen primers were analyzed by RAPD for their ability to identify polymorphisms, and the three primers that gave the most polymorphisms were used for the study. Fifteen markers were identified and were shown to indicate fixed differences between the two subspecies. Intergrades of unknown origin were distinguishable from pure Florida and pure northern wild and hatchery stocks, as well as first generation intergrades (F1s). The RAPD analysis was more sensitive than traditional histochemical agarose gel electrophoresis for identification of largemouth bass subspecies.