Microsatellite markers were developed and applied for population study in Mekong river catfish (P. hypophthalmus). Further research on genetic variation and parentage assignment will support for better genetic management and seed quality improvement. In this study, eight microsatellite markers were used to analyse genetic variation and traceability of 30 full-sib families in catfish. High polymorphism of eight micro satellites was observed in 60 parents that the average number of allele per locus yvas 5.9. The total of 47 alleles were analysed by genotyping 8 microsatellites in 900 offsprings, however only 41 alleles were effective for parentage asignment in catfish. As result, 94 percent of the offspring were unambiguously assigned to single families while 6 percent were assigned to more than one family. All micro satellite makers, were effective for studying genetic variation and parentage assignment of catfish.