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In the present investigation, the genetic structure of four populations of Catla catla, sequences of mitochondrial gene, cytochrome b (cyto b) from four populations were sequenced and analyzed. The sequences of mitochondrial regions revealed high haplotype diversity and low nucleotide diversity. The lowest 249 polymorphic sites and 0.00 parsimony informative sites were detected in populations of Fish Federation Pond (CCFFB) whereas highest 330 polymorphic sites and 56 parsimony informative sites were detected in populations of Narmada River (CCNRH) in the cyto b gene sequences in Catla catla populations. The twelve different haplotypes were detected among the four populations studied, lowest population specific haplotype as 2.00 was observed in Fish Federation Pond (CCFFB) and highest was in Population of Narmada River and Tighra reservoir. Sequencing of cyto b gene revealed 12 number of haplotypes (h) with haplotype (gene) diversity (Hd) 0.8736 and nucleotide diversity (π) 0.6474. These data clearly indicated that, feral/wild population showing highest values of polymorphisms, parsimony, haplotype diversity showing good, healthy habitat is lotic water (Narmada River) and lentic water body (Tighra reservoir). The results also concluded that the partial cyto b is polymorphic and can be a potential marker to determine ecological habitat based genetic differentiation among the populations.

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