Abstract: The genetic variability of wild populations of green arowana (Scleropages formosus) from Tasek Bera Lake and Endau River and a captive stock of Malaysian golden arowana as an out-group population was studied. The average number of alleles per locus was low, ranging from 2.33 in the Endau River population to 2.56 in the Tasek Bera Lake population. Departures from Hardy-Weinberg equilibrium were observed in these three populations depending on the locus. Among nine loci, seven significantly deviated from Hardy-Weinberg Equilibrium (p<0.05) in the Tasek Bera Lake population whereas five significantly departed from HWE (p<0.05) in the Endau River population. A deficit of heterozygosity was observed from the analysis of these nine loci. This genetic data indicate the wild population may be under stress due to inbreeding, over fishing and deterioration in the breeding environment. The estimates of FST and RST were statistically greater than zero for each comparison and this suggested the existence of three genetically distinct populations. However, the values of FST is low between Tasek Bera Lake and Endau River populations, reflecting historical patterns of connections between river systems in Peninsular Malaysia.