Paramphistomiasis is a serious disease of domestic and wild ruminants worldwide. The present study adopted an integrated approach based on the conventional histological features of muscular organs, tegumental topology and molecular analysis for identification of the flukes. Adult parasites were collected from the rumen of naturally infected cattle at Al Amrya abattoir and processed for different analyses according to standard methods. The flukes were conical-shaped, concave ventrally and convex dorsally. Based on the histological features of the muscular organs (pharynx, genital atrium and acetebulum), the flukes were identified as Calicophoron microbothrium (Family Paramphistomidae). The surface tegumental architecture was studied by scanning electron microscopy. Histological and morphological description was substantiated by molecular analysis based on PCR-sequence approach of the second internal transcribed spacer region (ITS2) of the collected flukes. Phylogenic tree was inferred based on the generated sequences and references in the gene bank.