Sarcocystis is the most common intracellular cyst-forming protozoan that infects the cardiac, smooth and striated muscles of animals and humans. This parasite has a significant economic, veterinary and medical impact in many regions of the world. The current study aimed to identify Sarcocystis species in domestic sheep and domestic goats slaughtered at the slaughterhouses of Duhok province in Iraq, from May 2021 to June 2022 by using molecular study. A total of 250 tissue samples collected from 147 sheep and 103 goats' different organs (79 esophagi, 105 skeletal muscles and 66 hearts) were examined for detection of sarcocysts through microscopic examination of fresh muscle tissues. Consequently, the isolated zoitocysts of sarcocysts and/or their fragments from each infected host were further used for molecular identification. Overall, 98.32% of the examined sheep and 98.06% of the examined goats were microscopically found to be positive for Sarcocystis species. Molecular identification of Sarcocystis spp. isolates based on analysis of the 18S rRNA gene sequences revealed the existence of S. tenella in both sheep and goats and S. capracanis in goats only. Alignment and phylogenetic analysis of the isolates in this study showed a very close relationship and close matching with other Sarcocystis DNA sequences which were available in the GenBank database. Results of the phylogenetic analysis showed sequences of S. tenella as a monophyletic cluster to the sequences of S. capracanis. As the 18S rRNA sequences of S. tenella and S. capracanis showed high similarity with each other, further molecular studies based on the cox1 and ITS1 regions are required for the exact characterization of species identified in the present study. Due to cross-infection and high incidence of Sarcocystis spp. in both sheep and goats in the world and in Iraq, development of disease control and prevention measures would be essential.