This study aimed to identify the diversity of Babesia and Theileria species in sheep across various regions of Iran using microscopic and molecular techniques, including species-specific PCR and enzymatic digestion. A total of 373 blood samples were collected from sheep during the tick vector activity period, from 2018 to 2021, in provinces such as Tehran, Alborz, Qazvin, Hamedan, West Azerbaijan, Kerman, and Fars.Results showed that 101 samples (27 %) exhibited piroplasms including 78 samples of Theileria spp. and 23 samples of Babesia spp. A molecular approach using general primers detected piroplasm parasites in 145 samples (38 %). Theileria ovis was notably present in 91 samples (24.39 %), followed by Theileria lestoquardi in 24 samples (6.43 %). Babesia ovis infection was detected in 30 samples (8.4 %). Despite extensive molecular evaluation, no other Babesia species, including Babesia motasi, were identified. Co-infections involving T. ovis and T. lestoquardi (4 samples; 1.07 %) and T. ovis and B. ovis (6 samples; 1.60 %) were observed. No Babesia spp. were detected in Kerman and Fars provinces, although T. ovis and T. lestoquardi were present.Blast analysis of the sequences indicated 100 % intra-species similarity, with inter-species similarities of 83.3 % (B. ovis and T. lestoquardi), 84.4 % (B. ovis and T. ovis), and 96.44 % (T. ovis and T. lestoquardi). In conclusion, B. ovis was the main cause of Babesiosis, while Theileriosis was predominantly attributed to T. ovis and T. lestoquardi. Molecular diagnostics play a key role in accurately distinguishing between these species, particularly in cases of co-infection involving Babesia spp. and Theileria spp.