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Buffaloes were screened for theileriosis by routine microscopic examination and also subjected for characterisation by PCR technique. Blood samples were collected from lactating buffaloes in post partum period from endemic areas of Athagarh block of Cuttack district, Odisha, India. Genomic DNA of Theileria piroplasm was isolated and genus specific primers were used for amplification of small subunit ribosomal RNA sequences. The amplified PCR products of Theileria spp. were sequenced. Out of 86 cases examined, 21 and 31 samples were found positive by Giemsa stained blood smear method and PCR technique respectively. The PCR product was sequenced and analysed for homology. The identified nucleotide sequence had close sequence homology with Theileria orientalis and Theileria buffeli. These findings also support the fact that 18S small subunit rRNA gene is hyper variable among the species. The nucleotide sequence was submitted to NCBI and a new accession number (MN262069) was assigned.