The size of the amplified product of Clinostomum schizothoraxi was found 544 bp long and the sequence obtained was submitted to GenBank and their accession number acquired was AF973619. This species also showed 47% G+C content which reflects that they are also stable at high temperature. Specimens of Clinostomum schizothoraxi was found in fish hosts of Carassius carassius, Schizothorax niger, S. esocinus, S. curvifrons and S. plagiostomus as is evident from the NJ phylogenetic tree, which means that there is some correlation between Monogenean and Digenean parasites as far as their hosts are concerned. Clinostomum schizothoraxi showed different chromosome number as well as chromosome morphology as compared to that of Monogeneans. It Possess 20 numbers of diploid chromosomes (2n=20). First pair of chromosomes is metacentric; pairs 2 & 3 are submetacentric; pairs 4, 5 & 6 are subtelocentric and pairs 7, 8, 9 and 10 are acrocentric. The smallest chromosome measured 5.88 μm and the largest 9.15μm. Number of chromosome arms (NF) are to be 26 in number; total haploid complement length (TCL) is 77.12 μm. Arm ratio of the complement ranges between 1.51–18.31 and the centromeric index ranges from 5.18–39.88. The karyotype formulla (K) can been written as 2n=20=1m+2sm+3t+4a. This species has been studied for the first time with respect to molecular and chromosome analysis.