This study was mapping the genetic diversity of Cirrhinus mrigala by using molecular markers for the ATPase 6/8 gene region. Samples of the target fish specie were collected from the different sites at the Indus riverine system of the Pakistan i.e Chenab (Head Qadirabad), Jhelum(Head Rasul), Ravi(Head Balloki) and Indus (Head Taunsa). Morphommetric parameters viz., Body weight, Girth, Total Length, Fork Length,Head length, Lengths of Caudal, Pectoral, Ventral Fins were recorded manually using measuring scale. After recording morphometric parameters blood from fish samples was drawn from caudal fin of the Fish, collected in Vautainer and immediately transferred into the Lab of IBBT where it is preserved in -80C for future use in DNA extraction. Phenol Chloroform Method of Genomic DNA extraction was used to extract whole blood DNA. The extracted DNA of the samples was run on 0.8% agarose gel by using electrophoresis of the DNA. Nanodrop was used to find out the concentration of DNA after that DNA was diluted according to the Need with deionized water. The PCR of ATPase 6/8 primers were used to amplify the target gene. The PCR product was confirm on 1.2% agarose gel. These gels were visualized in UV light and photographs were taken by Gel Documentation System (BIO-RAD, Gel-DOC EZ imager). After the visualizing of quality of band confirmation the samples were sent to be sequencing. The Analysis of Variance (ANOVA) for the different morphometric parameters was done by XLSTAT 2012 version 1.02. ANOVA results showed that all the morphomteric parameters were highly significant (p<0.01) within as well as between the groups. Pearson correlation analysis off overall population show that the body weight is positively correlated with the Fork Length, Total Length, Ventral Fin length, caudal Fin Length, Girth, with significant difference. Fork length is positively correlated with Total length, Ventral
Fin Length, Caudal Fin length, Pectoral Fin Length, with significant difference among other parameters. Total Length is positively correlated with Girth, Pectoral Fin Length, Ventral Fin Length, Caudal Fin Length, Girth, and Weight with significant difference among them. NJ methods suggested that existed relationship among different species located at different geographical locations. They all have a common ancestry. A strong relationship exists between fish species collected from different locations at Indus riverine system of Pakistan.