Fasciola worms were collected from livers of sheep and cattle and were subjected to morphological and metric assessment of external features of fresh adults, morphological and metric assessment of internal anatomy of stained mounted worms, determination of electrophorezed bands of crude adult homogenates and molecular characterization of species specific DNA segments using RFLP-PCR. The conventional morphological parameters for species determination of Fasciola spp. endemic in Egypt were evaluated versus protein bands characterization and genotyping. It was concluded that conventional morphological and metric assessments were not useful for differentiation between F. gigantica and F. hepatica due to extensive overlap in the relative ranges. Similar conclusion was reached concerning protein band characterization where the patterns of protein banding were mostly similar. In contrast genotyping using RFLP-PCR gave consistent results and clear differentiation between the two species. Considering the implications of proper speciation of endemic parasites on clinical evaluation, therapy, epidemiology and control measures, speciation of parasites is currently revised on molecular basis. The presently used molecular tool is therefore recommended for further study to help draw a proper map for geographical distribution of Fasciola species.