The usefulness of isozyme and protein markers in identifying tilapia species and their hybrids is demonstrated Genetic characterization of Oreochromis niloticus populations from commercial farms, experimental stations, and government hatcheries in Luzon, Visayas and Mindanao in the Philippines indicates well-established introgression with O mossambicus Genetic differentiation of the O niloticus stocks, measured by Nei's genetic distance, was highly correlated with O mossambicus gene content The implications of these results for tilapia genetic improvement are discussed.