Liver flukes from the genus Fasciola are the causative agents for human and livestock fascioliasis. Accurate identification of Fasciola spp. is essential to understanding the epidemiology of fascioliasis. This study aimed to determine the morphometric and molecular characterization of Fasciola spp. in livestock from Northwestern provinces of Iran. Five hundred adult Fasciola flukes were obtained from different definitive hosts (cattle, sheep, goats, and buffaloes) in four local abattoirs in the northwestern provinces of Iran (West-Azerbaijan, East-Azerbaijan, Ardabil, and Zanjan) from September 2021 to August 2022. All samples were examined by morphometric criteria; then, 49 samples were identified using PCR-RFLP based on ITS1 region and 23 sequence of isolates analyzed by cox1 marker. PCR-RFLP methods compared morphometric results, and cox1 gene sequences were used to confirm PCR-RFLP results and phylogenetic analysis. The differences between the body length, body width, cephalic cone length, cephalic cone width, body area, and distance between the ventral sucker and posterior end of the body in two species were significant (p < 0.05). Based on the morphometric criteria, 139 samples (27.8%) were identified as Fasciola gigantica and 361 (72.2%) as Fasciola hepatica. Similarly, PCR-RFLP analysis of ITS1 region confirmed morphometric results. No hybrid forms of Fasciola were detected. Partial sequences of cox1 showed 13 variable sites with eight haplotypes in F. hepatica and 12 variable sites with five haplotypes in F. gigantica. Based on the results of this study, the PCR-RFLP method can be used to confirm the morphological method of Fasciola species, but it is insufficient to study their genetic diversity. Also, sequences of cox1 results of the present study showed that F. hepatica and F. gigantica species in the Northern provinces of Iran have different genetic structures and haplotypes.