Background: Babesiosis in dogs is endemic in tropical countries like India because of presence of tick vectors as well as reservoir stray dog population round the year. There is paucity of information regarding the prevalence and molecular confirmation of Babesia species in dogs in Andhra Pradesh. The present study was aimed to detect Babesia species in naturally infected dogs in Andhra Pradesh.Methods: During the one-year study i.e. from June 2019 to July 2020, blood samples were collected from 442 tick infected dogs showing clinical signs suggestive of babesiosis to determine the prevalence of Babesia species by microscopy and molecular technique. Factors associated with prevalence of babesiosis were analyzed by logistic regression models.Result: Microscopic examination of stained blood smears revealed 11.8% prevalence of Babesia spp. infection in dogs in the study area, while 28.3% of dogs were found to be positive for Babesia spp. in the first Babesia genus-specific PCR. Further analysis of positive samples with species-specific PCR, Babesia gibsoni and B. vogeli were detected 19.9% and 8.6% of dogs, respectively. Risk factor analysis by binary logistic regression model revealed that the living condition of the dogs, gender, age, medium and tick infestation as risk factors for B. gibsoni and B. vogeli infection.