The species of liver flukes of the genus Fasciola (Platyhelminthes: Digenea: Fasciolidae) are obligate parasitic trematodes residing in the large biliary ducts of herbivorous mammals. While Fasciola hepatica has a cosmopolitan distribution, the other major species, i.e., Fasciola gigantica is reportedly prevalent in the tropical and subtropical regions of Africa and Asia. To determine the phylogenic location of Fasciola sp. of Assam (India) origin based on rDNA molecular data, ribosomal ITS regions were sequenced and compared with other species of trematodes in the family Fasciolidae. NCBI databases were used for sequence homology analysis using BLAST and ClustalW programs. The phylogenetic trees constructed based upon the ITS (1 and 2) sequences revealed a close relationship with isolates of F. gigantica from China, Indonesia, Japan, Egypt, and Zambia, the isolate from China with significant bootstrap values being the closest. Using the novel approach of molecular morphometrics that is based on ITS2 secondary structure homologies, phylogenetic relationships of the various isolates of fasciolid species have also been discussed. While comparing ITS1, the sequence of another Indian isolate designated as F. gigantica (accession no. EF198867) showed almost absolute match with F. hepatica. Hence, this particular isolate should be identified as F. hepatica and not F. gigantica.