Animal and human fascioliasis is a health and economic problem in few of tropical and subtropical areas of the world, including Iran. The present study aimed to determine the genotype diversity of isolates in different hosts from Gilan province, northern Iran, and compare it with those isolates from southwestern Iran. Forty-eight adult spp. were collected from cattle, sheep, and goats from slaughterhouse in Talesh, north of Iran. DNA was extracted from each fluke and PCR-RFLP was used to find out the species of the isolates. The ribosomal ITS1 and ITS2, and mitochondrial genes of NDI and COI from individual isolates of each host were PCR-amplified and the PCR products were sequenced. Genetic variation within and between the isolates was evaluated by comparing the sequences of ribosomal and mitochondrial genes. For analysis of phylogenetic diversity of the flukes, phylogenetic trees were constructed, using ITS1, ITS2, NDI, and COI sequences of the isolates. Based on PCR-RFLP profile, 5 (22.7%) of the total of sheep isolates and 18 (90%) of cattle isolates were identified as and other remaining samples from sheep, cattle and goats were identified as . Based on ITS1 and ITS2 sequences, six and seven nucleotide polymorphism were respectively noted in the isolates. On the other hand, CO1 region sequences showed considerable variation, which laid Talesh (north) isolates in a separate cluster. Findings of the study showed that the sequences of CO1 isolates from north and southwest have substantial differences mainly in CO1 region.