Babesia vogeli infection is an important tick-borne haemoprotozoan disease of canids. The study was carried out to understand the prevalence and molecular phylogeny of B. vogeli in pet dogs. A total of 128 blood samples were collected during study period. The microscopy based prevalence of 7.81% was recorded for large form of Babesia spp. We developed and standardized heat shock protein (hsp) 70 genebased PCR assay with high analytical sensitivity and specificity tested with B. gibsoni, H. canis and D. repens. The PCR assay on all the blood samples revealed higher prevalence rate of 25% of B. vogeli infection. The correlation analysis for age, breed, sex and presence of ticks on animal body did not reveal significant association with B. vogeliinfection, and among the clinical factors, only pale mucus membrane was significantly associated with presence of infection. The sequence analysis revealed 99.8 - 99.9% identity among themselves and 99.8 - 100% similarity with the published sequences of B. vogeli. Phylogenetically, all the Indian isolates clustered together with Japan and Taiwan isolates, indicating genetically similar species circulation in Asian content. In conclusion, in addition to clinical and microscopic examination, the PCR assay is recommended for confirmatory diagnosis of B. vogeli infection as genetically similar species are circulating in dogs.