Equine piroplasmosis, caused by Babesia (Theileria) equi, is well reported from many parts of India. However, literature regarding its prevalence from semi arid India is limited. Alongside, there is complete absence of information about genetic characterization of B.(T.) equi and the associated genotypes from India. In the present study, the prevalence of B.(T.) equi was studied from semi arid India using 18S ribosomal gene based PCR assay. An overall prevalence rate of 10.46% was recorded. PCR was more sensitive and specific in comparison with blood smears. The found isolates were sequenced. These sequences were aligned and submitted into NCBI. All the isolates showed 100% homology with each other and represented a single haplotype. When compared with other isolates of B.(T.) equi across India and globe, using Genetool and Mega 6 softwares, they showed 99.5-99.2% and 95.7-97.0% homologies, respectively. A unique substitution of G by A at 206 nucleotide position was reported in all found isolates in comparison to earlier reported isolates from India. The studied isolates were found to be phylogenetically closer to isolates from USA and Trinidad than to other parts of the world. All the Indian isolates belonged to genotype A of B.(T.) equi.