Fascioliasis caused by Fasciola species (Fasciola hepatica and Fasciola gigantica) is considered as the most important helminthic infection of domestic animals in developing countries. The present study was performed during January to December 2019, in Biology Department, University of Zakho. Hundred adult’s flukes of Fasciola spp. were isolated from bile ducts and gallbladder of cattle, sheep and goats slaughtered at different abattoirs (Duhok, Zakho, Shelidiza, Aqrah and Bardarash) in Duhok governorate, Kurdistan region, Iraq. Genomic DNA extraction was performed using a Genomic DNA Extraction kit, Jena Bioscience GmbH (Germany). Specific markers ITS1 and ITS2 ribosomal DNA were used for amplifying 480 and 550 bps fragments.  DNA sequences have been used to characterize these liver flukes. The PCR products were separated by electrophoresis in 1.5% agarose gel, visualized by staining with RedSafe dye, and photographed. ITS-1 and ITS-1 markers were amplified successfully, the length of produced band for ITS-1 was 480 bp and for ITS-2 was 550 bp. Thirteen Fasciola spp. flukes isolated from cattle, sheep and goats from different districts were sequenced, from these thirteen PCR products, 7 amplicons were recognized as Fasciola hepatica and 6 amplicons as Fasciola gigantica. These sequences were deposited in GenBank under accession numbers: MW161261, MW084365, MW052601 MW084349, MW082585, MW084348, MW082830 for F. hepatica and MW161260, MW052602, MW084353, MW084350, MW082589, MW085034 for F. gigantica. This study confirms the prevalence of Fasciola hepatica and Fasciola gigantica in Iraq by using the ITS-1 and ITS-2 rDNA.