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Four microsatellite loci were identified for Clarias macrocephalus and the forward and reverse primers for each locus were designed according to their unique flanking regions. One locus, Cma-1 *, was monomorphic, three loci, Cma-2*, Cma-3 * and Cma-4*, were polymorphic having 5, 14 and 30 al leles per locus respectively. The polymorphic microsatellite loci were studied in four natural populations of C. macrocephalus collected from different locations in Thailand. Mean number of alleles per locus were 8.0, 8.7, 6.0 and 10.0, respective to populations from Pattani, Pattalung, Chiangrai and Prachin buri. Mean heterozygosities were 0.744, 0.765, 0.718 and 0.810 respectively. Nei's genetic distance showed the closest relationship between Pattalung and Prachinburi (0.230) and the largest genetic dis tance between Pattalung and Chiangrai (0.535). However, the genetic distances obtained in this study were not accorded with geographic distance.

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