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In Pakistan the work on genetic of different populations of Channa marulius have not been performed so for and the Clustering analysis was done to find out the intraspecific variations among different populations of Channa marulius using Pearson Correlation Coefficient method based on Unweighted Pair Group Method with Arithmetic Mean (UPGMA) by XLSTAT 2012 (version 1.02). 50 samples of C. marulius populations were collected from five different geographical sites of natural waters viz., Chashma Barrage at River Indus (District Mianwali), Qadirabad Barrage at the River Chenab (District Gujranwala), Balloki Barrage at River Ravi (District Kasur), Trimmu Barrage at the junction of Chenab and Jhelum Rivers (District Jhang) and Taunsa Barrage at Indus River (Tehsil Kot Addu District Muzaffar Garh). Dendrogram generated by RAPD data of representative samples of each site divided the populations of C. marulius into four major clusters. The results of the studies clearly indicate that variance decomposition for the optimal classification values remained as, 65.90% for within class variation while 34.10% for the between class differences. The distance between the class/cluster centroids was 1.737 for class 1 and 2, 1.105 for 1 and 3, 1.009 for 1 and 4, 1.500 for class 2 and 3, 2.000 for 2 and 4, while this distance between class 3 and 4 was 1.500. Quantifiable differentiation among various species of C. marulius revealed the impacts of changing environment and other possible factors. [ABSTRACT FROM AUTHOR]