To conserve the fish biodiversity, there is urgent need to study the genetic diversity of natural fish stocks for successful fishery management, conservation, and rehabilitation of the species. For this purpose, the present study was planned to evaluate the use of the RAPD assay to generate the species specific profile, to estimate the genetic similarity/variation and to examine the genomic variation based on RAPD data and the population genetic structure for conservation of five carnivorous fishes named Channa punctatus, Channa marulius, Sperata seenghala, Rita rita and Wallago attu. The fish samples for this study were collected from Chashma Barrage at River Indus near District Mianwali, Qadirabad Barrage at Chenab River in Tehsil Wazirabad, District Gujranwala, Baloki Barrage at Ravi River in Tehsil Bhai Pharo District Kasur, Trimu Barrage at the junction of Chenab and Jhelum Rivers in District Jhang and Taunsa Barrage at Indus River in Tehsil Kot Addu, District Muzaffar Garh. Morphometric parameters of the collected fish specimens, were measured and the data was subjected to ANOVA and multivariate Principle Component Analysis (PCA). Physicochemical parameters of the water bodies such as Water Temperature, Electrical Conductivity, pH, Dissolved Oxygen, Salinity at the spot and Total Dissolved Solids (T.D.S.), Total Alkalinity, Total Hardness, were measuredfrom the water samples brought to the lab and noted. Correlation was calculated with the help of computer. The DNA from these fish specimens was extracted by modified salt extraction method and its presence was qualitatively measured with the gel electrophoreses. PCR was performed in the lab. Binary data of the RAPD for different species were subjected to XLSTAT-2012, version 1.02 and Dendrogram were generated. The binary data was further analyzed for diversity indices and Principle Component Analysis (PCA). The morphometric data of stoutness and average length of paired pectoral fin length in the ANOVA show significant difference in case of Channa punctatus. All studied parameters were significantly different in S. seenghala and non-significant in Channa marulius, Rita rita and Wallago attu. When the PCA was performed for the morphometric parameters, C. punctatus divided into four factors, first two main factors accounted for 98.706% of cumulative variability, in C. marulius, divided into six factors with first two main factors accounted for 99.996%, in tested variables of the R. rita division was into eight factors with two main components, which accounted for 99.02%, in case of S. seenghala, tested variables divided into nine factors with two main components, accounted for 99.91% and in case of W. attu divided into four factors with first two main factors which accounted for 99.996% of cumulative variability. The correlation for different physicochemical parameters between different sampling sites showed that pH with water temperature (r = 0.107) and dissolved oxygen (r = 0.905) was positively non-significant while the correlation with electrical conductivity (r = -0.798), salinity (r = -0.888), total dissolved solids (r = -0.857), total alkalinity (r = -0.736) and total hardness (r = -0.499) was negatively non-significant. The electrical conductivity was positively correlated with all the physic-chemical parameters as with water temperature (r = 0.482), salinity (r = 0.925), total dissolved solids (r = 0.889), total alkalinity (r = 0.452) and total hardness (r = 0.906) and this correlation was non-significant. The correlation between the total alkalinity and total hardness was also positive and non-significant (r = 0.048). The number of bands for PCR products in Channa punctatus ranged as low as three to a maximum of seven, with an average of 6 bands per primer. The number of polymorphic bands per primer was 1 to 3 with 14.29% to 50%. The number of bands in Channa marulius ranged as low as three to a maximum of seven, with an average of 6 bands per primer with 1 to 3 polymorphic bands. The polymorphic bands ranged from 14.29% to 50%. The number of bands in Rita rita ranged as low as three to a maximum of seven, with an average of 6 bands per primer with 1 to 3 polymorphic bands. The polymorphic bands ranged from 14.29% to 50%. The bands were as low as three to a maximum of seven, with an average of 6 bands per primer in Sperata seenghala with 1 to 4 polymorphic bands. The polymorphic bands in these populations ranged from 14.29% to 57.14%. The number of bands produced in Wallago attu, ranged from three to seven, with an average of 6 bands and 1 to 4 polymorphic bands per primer were observed. The polymorphic bands in these populations ranged from 14.29% to 66.67%. The dendrogram for C. punctatus divided the randomly selected individuals of the five populations into four classes/clusters; 17 members in first cluster/class, 4 samples in second cluster/class and 2 samples in the third and fourth class/cluster. The randomly selected individuals of the five populations of C. marulius were divided into four classes/clusters; 21 in 1st, 2 in 3rd and one in 2nd and 4th class, each. The populations of R. rita were divided into four classes/clusters as in C. marulius. In S. seenghala four clusters with 21 in 1st, 2 in 2nd and one in 3rd and 4th class, each. In W. attu, into six classes/clusters. i.e., 16 individuals in 1st class/cluster, 3 individuals in 2nd and 4th Class/cluster, each, while in 3rd, 5th and 6th were only one individual, each. The PCA regarding variability for C. punctatus indicated eleven factors, first four main factors accounted for 55.849%. The first and second group (F1 and F2) accounted for 14.881% each. Contribution for polymorphism amongst the randomly selected individuals of five populations divided the role of primers into four major variable groups, one group towards the positive side, one towards negative and two groups at the neutral distinction. According to the Kaiser (1958) criterion based upon the Eigen values, first three main factors out of eleven, accounted for 42.77% of cumulative variability in C. marulius. Contribution for polymorphism amongst the randomly selected individuals of five populations divided the role of primers into five major variable groups, two groups towards the positive side, two towards negative and one group at the neutral distinction. Rita rita populations were divided into nine factors/groups and first two main factors accounted for 30.968% of cumulative variability. Th trend divided the role of primers into five major variable groups, three groups towards the positive and one group towards the negative while the remaining at the neutral distinction. In same way, S. seenghala was devided into twelve out of which four main components all together accounted for 55.41% of the cumulative variation. The first and second group (F1 and F2) accounted for 15.717% and 14.044% respectively, of the cumulative variability. The trend for polymorphism divided the role of primers into seven major variable groups, two groups towards the positive side and four groups towards the negative side and one got the neutral distinction. Data in W. attu was divided into thirteen components and four main factors accounted for 50.37% of the cumulative variation in W attu. The trend divided the role of primers into four major variable groups, one group towards positive side, one groups toward negative side and two groups has the neutral distinction. The specimen Tsa1 shows complete distinction in all species except for C. punctatus. Knowledge of genetic structure of the major River populations is helpful for management of the populations in order to maintain their genetic quality. In this study the results indicate good correspondence in the data analyses of morphometric parameters, and RAPD molecular markers using various statistical techniques with the exception of the distinction of individuals from different sites, which clearly indicated some environmental impacts, are likely influencing the genetic makeup within and between the local populations. This study also has provided the genetic information of the present fish populations from and how evolutionary processes are affecting the fish fauna. So this study along with the strengthening of the academic research area will also prove an applied research which will help the breeders to choose most fit candidates for the breeding program in the Pakistan." xml:lang="en_US