Theileriosis is a severe and often fatal protozoan tick-borne disease of ruminants. It is distributed worldwide, causing high morbidity and mortality leading to high economic losses. Basic information on the parasite species and vectors are lacking, and pathogenicity of the disease is poorly understood in the Sultanate of Oman. This study was carried out in Al-Batinah and A'Dakheliya regions to identify Theileria species in Omani sheep, using "Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP), to identify the ticks infesting the sheep and to determine the incidence and distribution of theileriosis in Al-Batinah and A'Dakheliya regions. Whole blood (Ethylene diamine tetra-acetic acid (EDTA) and citrated blood), and ticks, were collected from 231 animals. Necropsies were carried out in 11 indigenous sheep. Specimens including liver, lungs, spleen, lymph nodes, and adrenal glands were collected for impression smears, histopathology, and transmission electron microscopy study (TEM) and Polymerase Chain Reaction (PCR). Blood in EDTA tube was examined microscopically for piroplasm detection and blood parameters including Packed Cell Volume (PCV), Red Blood Cells count (RBC), Haemoglobin (Hb), and White Blood Cells count (WBCs) were determined. Deoxyribonucleic acid (DNA) was extracted from citrated blood, amplified and Theileria was detected using nested PCR followed by RFLP. The results of this study indicated that theileriosis in indigenous sheep may fall into three forms, peracute, subacute or chronic. Splenomegaly, jaundice and enlargement of the liver, which appears yellowish with a friable texture and contained grayish foci, were seen. Impression smears revealed an intra and extra-cytoplasmic schizonts in the lungs, liver, spleen, lymph nodes and adrenal gland. Transmission electron microscopy of the lungs showed schizonts in the lymphocyte and sin erythrocytes. PCR of tissues revealed the presence of Theileria lestoquardı. A total of 87% (201/231) of blood samples were positive for schizonts by microscopic examination. In nested PCR analysis of DNA samples extracted from 231 samples, 62.3% (144/231) were positive. A total of 54.5% (126/231), 7.8% (18/231), 32.5% (75/231) and 5.19% (12/231) were positive for both PCR and schizonts, positive PCR but negative schizonts, negative PCR but positive schizonts and negative in both PCR and schizonts respectively. RFLP was used for the identification of Theileria species. The study revealed the presence of Theileria lestoguardi, Theileria ovis and mixed infections of Theileria lestoquardi, Theileria annulata and Theileria ovis species. Out of 144 DNA extracted, 61.1% (88/144), 27.1% (39/144), 11.8% (17/144) were positive for Theileria ovis, mixed infections (T. lestoquardi, T. annulata and T. ovis) and T. lestoguardi respectively. Animals infected with T. ovis and mixed infections of T. ovis, T. annulata and T. lestoquardi had significantly lower (P < 0.0001) RBCs, Hb and PCV compared to the non-infected animals, however, T. lestoquardi was associated with significant reduction in PCV (P<0.05) but not in RBC, Hb and WBC. Out of 231 of animals 20.8% (48/231) were infested with ticks. A total of 35.3% (6/17), 15.9% (14/88), and 23.1% (9/39) of samples infected with T. lestoquardi, T. ovis and mixed infections of T. lestoguardi, T. annulata and T. ovis were infested with ticks respectively. As there may be other species of Theileria and other possible vectors of the disease, further studies are recommended to cover more regions with more number of animal included.