Coenurus cerebralis is a metacestode larval stage of Taenia multiceps that inhabits the central nervous system of their intermediate host, especially sheep and goats. This study aimed to investigate the molecular prevalence of C. cerebralis in sheep in Iğdır province. Out of 1300 sheep brought to the slaughterhouse, 300 sheep were selected based on the clinical signs of coenurosis. After slaughtering, the sheep heads were brought to the laboratory to observe cysts' presence and collect the specimens for PCR analysis. Cysts were present in 246/300 sheep brains, with 112 cysts in the left hemisphere, 73 in the right hemisphere, 12 in the cerebellum, and 9 in the brain stem. However, 40 cysts were observed in both hemispheres. PCR analysis by amplifying COX1 gene revealed that 243 samples were truly positive for C. cerebralis. Sequencing and phylogenetic analysis of two sequences (PP713059, PP711257) showed 100% similarity with the sequence of C. cerebralis (KX547654.1) and one sequence (PP711299) showed 99.19% similarity with the sequence of C. cerebralis (KX547656.1) isolated from China. Our obtained sequences were included in the same clade with six other clade members in the phylogenetic tree. Among different parameters, it was observed that the prevalence was higher in males and animals with less than 1 year of age. Similarly, the prevalence was higher in winter, followed by autumn, spring, and summer. The current study illustrated a high rate of coenurosis infection in the sheep population of Iğdır, Turkey. Preventive measures should be followed to avoid the transmission of this parasite to healthy sheep and other intermediate hosts including humans.