Haemoprotozoan and haemorickettsial diseases like trypanosomosis, theileriosis, babesiosis, anaplasmosis and ehrlichiosis are important diseases of cattle and cause huge economic loss to the livestock industry. Cattle and other animals are being regularly traded across the porous Indo-Bhutan border districts of Assam. The present study was conducted to confirm the haemoparasites species of cattle recorded in 4 districts of Assam along the border. PCR analysis amplified Theileria orientalis DNA both from blood and eggs of Rhipicephalus (Boophilus). microplus tick and Babesia bigemina and Anaplasma marginale from blood. Phylogenetic analysis revealed T. orientalis isolate having 98.83% and 99.00% similarity with isolates reported from Vietnam and Myanmar, a new B. bigemina isolate and A. marginale isolate bearing 93.46% similarity with isolates from USA and Mexico.