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Freshwater Pangasiid catfish species and hybrids are difficult to identify on the basis of morphological characteristics, especially for larvae and fingerlings. In this study, we identified genetic markers for Pangasiid catfish breeds, viz. Pagasianodon gigas, Pagasianodon hypophthalmus and their F1 and F 2 hybrids. Twenty primer comb inations were used to screen for specific amplified fragment length polymorphism (AFLP) markers. A total of 486 DNA bands were identified and 335 polymorphic bands were found to be segregated among these catfish types. The level of polymorphism detected using 20 different primer combinations ranged between 65.38-100%. Eleven distinct markers were found to be significantly associated with P. gigas (two markers), P. hypophthalmus (three markers), their F1 hybrid (three markers) and F2 hybrid (three markers). Using these markers, 100% of the individuals were accurately assigned to their correct species. These results demonstrate that AFLP markers can be used to genetically i dentify Pangasiid catfish species and hybrids.