Corbicula fluminea is a spread freshwater bivalve with high nutritional and medical values. The present study aimed to investigate the molecular diversity within the collected four morphs of C. fluminea from the River Nile in Egypt by using RAPD-PCR biomarkers. The genetic polymorphism among their amplified DNA fingerprints of the four forms of C. fluminea population was performed by applying an available online program; Jaccard-Needham dissimilarity distance. These four morphotypeshells were also statistically distinguished morphologically and morphometrically depending on their colour pattern, and measurements of their lengths, heights and widths. Furthermore, the cluster analysis of the phenogram software program was documented for determining the phylogenetics. The biometric parameters and genetic distances manifested two major clusters of C. fluminea. The first major cluster had only one variety {Morph-I} with the highest ratio of genetic distance 0.9 reflecting a great genetic distance with other three varieties. The second major cluster has three polymorphics and again divided into two minor clusters. One minor cluster, further divided into two varieties {Morph-III & Morph-IV} and other having only one variety {Morph-II}. Hence, the study assessed and established a relatively DNA barcode reference of that molecular clam diversity.