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Genetic investigation in fish population is usefull not only to find changes in genetics of species but also to improve management and stock program. Changes in genetics may be either by mutagens or by evolution. Genetic based discrimination among fishes or any other organism by using molecular markers goes back to about 3 decades. Microsatellite markers owing to great variability, supreme divergency and co dominant capacity are widely used in genetic studies. Genetic diversity of Catla catla (Thaila fish) from various sites of two rivers Indus and Chenab (Pakistan) was determined by using 11 single sequence repeat (SSR) markers against 15 samples. Out of 213 loci detected 195 were polymorphic in all samples in this way mean value of polymorphism for all used markers was 91.54 %. Value of effective alleles number (NE ) ranged 1 ? 8 with average of 4.0909, allelic frequency or Shanon Information Index (I) was 0.2667 -1.0000 with mean of 0.5455. Gene diversity or Nei?s genetic diversity (HE ) was 0.0000 -- 0.8356 with mean of 0.5713 while value of PIC (Polymorphism Information Content) ranged 0.0000 --0.8152 with mean of 0.5261. Maximum frequency based genetic distance was 0.9091, 0.8182 between various locality fishes of Chenab and Indus repectively. Similarly Jaccard?s similarity coefficient was 0.8182 and 0.7273 between various zone samples of Chenab and Indus respectively, and finaly phylogenetic tree analysis reflects genetic variations within and between populations of Catla catla of various zones of various rivers. This study indicates moderate genetic variations within and between Catla catla populations of various rivers and various zones of these two rivers. This genetic information is beneficient for proper administration of Catla population to maintain familial make up.
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