Fascioliasis is a zoonotic disease, caused by the parasites Fasciola (F.) hepatica and F. gigantica, which poses a great threat to the ruminants in addition to humans in many countries, including Iraq. Hence, the study of this parasite and its deleterious impacts on host, morphologically, histopathologically, epidemiologically, and molecularly, is so important. Hence, the current study was designed to investigate this fluke of livestock in Erbil and Halabja slaughterhouses from August to October 2022. To meet the prerequisites of the study, 33 flukes were collected from the sheep and cattle at study sites. The samples were transported to the Zoology Research Laboratory, Salahaddin University-Erbil, Iraq. Some of them were used for morphological identification, and others were preserved in 96% ethanol and stored at -20°C. Subsequently, DNA was extracted. Conversely, pieces of the infested liver were fixed in 99% ethanol and 10% formalin before histopathologic examination. The parasite species were identified using traditional Polymerase Chain Reaction (PCR), and sequencing methods. Macroscopically, hepatomegaly was the main finding of the infestation. Among livestock, cattle exhibited the highest rate of morbidity, followed by goats and sheep. The amplified DNA region was 98–99%, matched to F. hepatica and F. gigantica sequences. It was also established that 28S rDNA sequencing combined with morphologic characteristics of Fasciola species can be applied as a salient indicator in the identification of flukes. The current study is reckoned as a comprehensive investigation regarding fascioliasis, because it covered the parasite epidemiology, morphology, and molecular identification, despite of histopathologic examination.