Pangasius krempfi and Pangasius mekongensis are economically important species of catfish family Pangasiidae.Compared to P. mekongensis, P. krempfihas highervalues and has been cultured recently in the Mekong Delta, Viet Nam. Wild catfish fingerlings (P. krempfi and P. mekongensis, respectively. Nei’s genetic distance between the two species was 0.742 and their genetic difference GST was 0.655. Principal coordinates analysis showed that the two speciesclustered in two separate groups. The results indicate that six ISSR markers used in the present study can differentiate P. krempfi and P. mekongensis.