Monieziasis caused by Moniezia species is considered the most common gastrointestinal disorder in sheep. The present study was performed to determine the prevalence of the tapeworms in the sheep’s intestine in Duhok province, Kurdistan region, Iraq based on molecular techniques. A total of two hundred sheep were examined during the period from January to June 2022. Thirty-two (16%) sheep were harboring Moniezia species, while statistically local sheep were more susceptible to infection (32.3%) as compared to imported sheep (8.1%). Sampled tapeworms were analyzed morphologically and using conventional PCR for amplifying and sequencing of ITS 1 and cox1 gene. The results of PCR confirmed the identity of tapeworms as Moniezia spp. with a product length of 743 base pairs for ITS 1 and 364 base pairs for cox1 gene. The sequencing analysis using cox1 gene revealed that; 25 Moniezia expanse and 7 Avitellina centripunctata while sequence analysis by using ITS 1 gene revealed 20 Moniezia expanse and 12 Moniezia spp. with 99.6-100% homology. This study confirms the prevalence of Moniezia spp. in Iraq by using the ITS 1 and cox1 gene.