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Information on levels of genetic variation is a prerequisite for successful natural resource management and genetic improvement programs. In this study we aimed to identify genetically distinct stocks of North African catfish, Clarias gariepinus (Burchell, 1822) in Thailand which could be used as germplasm sources for a selective breeding program. Four hatchery stocks (n = 50 fish/population) were sampled, three from northeastern provinces (Sakon Nakhon, SN; Nong Khai, NK; and Nakhon Ratchasima, NR), and one from central Thailand (Nakhon Nayok, NY). Six microsatellite loci were scored using primers developed for this species. The results revealed significant genetic differentiation among stocks (F ST = 0.096; CI = 0.045-0.166) with all but one pair of stocks (NK vs SN) being significantly different, as shown by pair-wise F ST. Three stocks showed homozygote excess. Further analyses showed no recent bottlenecks, but some evidence of genotype disequilibrium. Allele diversity was low (A ranged from 6.00-7.00; A e ranged from 3.43-4.59) while heterozygosity was moderate (H o ranged from 0.52-0.72; H e ranged from 0.67-0.77). The effective population sizes (N e) based on linkage disequilibrium method were between 22.2 and 133 individuals. The neighbor-joining (NJ) tree was robust and revealed the closest genetic relationship between SN and NK, which were clearly separated from NR and NY. Two groups of stocks (northeastern, NK+NR+SN vs NY) showed highest variation among groups (13%) as revealed by AMOVA. The results apparently revealed genetically distinct stocks of North African catfish in Thailand which are useful for establishing a base population for a genetic improvement program.

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