Random amplified polymorphic DNA (RAPD) analysis was applied to individuals of Horabagrus brachysoma sampled from three geographic locations of Western Ghat river systems in India. Of the thirty-two 10-mer RAPD primers screened initially, ten were chosen and used in a comparative analysis of H. brachysoma collected from Chalakkudy, Meenachil and Nethravathi river systems. A total of 124 RAPD fragments were amplified, out of which 49 (39.51%) were found to be shared by individuals of all three river systems. The remaining 75 fragments were found to be polymorphic (60.48%). This confirms the suitability of RAPD markers for the study of population genetic structure in yellow catfish stocks
