The aim of the present study was to investigate the presence of Theileria in blood samples of crossbred and indigenous adult cows raised under unorganized small scale farming system in a Babesia and Anaplasma endemic geographical area from Assam, India and to see its transmission through Rhipicephalus (Boophilus) microplus ticks. For the present study, 57 clinical cases of cattle suspected to be of hemoparasitic infections were taken into consideration. The parasites were identified based on morphology in giemsa stained blood smear followed by polymerase chain reaction (PCR). Sera samples were tested for T. annulata antibodies in plate and Dot-ELISA. PCR was also conducted in eggs of Rhipicephalus (Boophilus) microplus tick collected from a Theileria orientalis positive animal. PCR amplified 1124, 776, and 160 bp DNA fragments of B. bigemina (64.91%), T. orientalis (21.05%) and A. marginale (14.03%), respectively. This assay further conducted in 12 T. orientalis positive blood samples with primers of Buffeli, Chitose, and Ikeda variants of T. orientalis showed 3 samples positive to Ikeda type and none for Buffeli and Chitose. Babesia bovis and Theileria annulata specific primers also did not amplify any fragment during the PCR assay of the blood samples. Further, all sera samples tested negative to T. annulata antibodies in Plate and Dot-ELISA. PCR conducted in eggs of R (B).microplus tick collected from a T. orientalis positive animal revealed presence of the parasite DNA. Gradual improvement in physical condition leading to complete recovery in 10 out of 12 T. orientalis infected clinical cases treated with buparvaquone(at 2.5mg/kg.b.wt I/M) was the feedback obtained from field veterinarians and the cattle owners. The present investigation represents the first report of occurrence of T. orientalis in cattle of Assam with involvement of pathogenic Ikeda strain in clinical outbreaks and its possible natural transmission by R (B). microplus through the transovarian mode.