Liver infections due to amphistomes in buffaloes cause significant economic losses in livestock sector. The present study investigated the classical morphological features of adult amphistomes combined with histopathology and molecular identity in slaughtered buffaloes from Khyber Pakhtunkhwa, Pakistan. Adult amphistome were collected and morphologically characterized as Gigantocotyle explanatum. Morphometric measurement (n=50) were obtained with 12.05+-1.68 mm in length and 5.77+-0.81 mm in width, and the values of sagittal section was 6.35+-1.03 * 2.98+-0.50 mm in size. Severe bile duct pathology was observed with fibrosis of the duct wall with an irregular epithelial border, hyperplasia and inflammatory response with numerous neutrophils and eosinophils. The molecular identity of G. explanatum within Paramphistomidae was confirmed by ITS-2 rDNA sequences phylogenetic analysis based on maximum likelihood method. The genetic data based on ITS-2 secondary structure of G. explanatum consisted of four helix, Helix I, II and IV were conserved as compared with other closely related reference taxa of family Paramphistomidae and Gastrothylacidae. Helix III expressed some variations. The study concluded that rDNA ITS-2 and secondary structure information provides a guide for other researchers to determine the molecular taxonomic position of Paramphistomidae trematodes, data will support future clinical studies and control measures to reduce the amphistomiasis in buffaloes.