Ticks are obligate blood-feeders that are vectors for several pathogens of public health and veterinary importance. Ticks were reported to have endosymbionts such as Coxiella-like, Francisella-like, Midichloria mitochondrii, Wolbachia, etc. With limited data on endosymbionts in ticks from India, we explored the endosymbiont diversity in ticks infesting the pets and livestock in Puducherry. Ectoparasites were collected from pet and domestic animals in 11 veterinary dispensaries between August to September 2022 and identified by taxonomical keys and sequencing of 16S rRNA, 18S rRNA, and Cytochrome oxidase subunit I genes. Wolbachia, Coxiella-like, Francisella-like and Midichloria mitochondrii endosymbionts were screened by PCR and their presence was confirmed by sequencing. A total of 984 ectoparasites including 5 tick, 3 lice, and 1 flea species were retrieved from 304 animals. Rhipicephalus sanguineus, Rhipicephalus haemaphysaloides, and Haemaphysalis bispinosa ticks were positive for the presence of Coxiella-like endosymbionts (CLEs) clustering under the clades B and C. Further, vertical transmission of CLEs in the field-collected R. sanguineus ticks was also demonstrated. This study offers an overview of the endosymbionts harbored by ticks in Puducherry with the first report of CLEs in H. bispinosa ticks and the transovarial transmission of endosymbionts in R. sanguineus ticks.