Background: Canine babesiosis is an emerging or re-emerging disease caused by Babesia and Theileria protozoans, also called piroplasms, transmitted by Ixodid ticks. In Europe, four etiological agents have been identified to date, namely Babesia canis, B. vogeli, B. gibsoni and Theileria annae. France has a high prevalence of canine babesiosis and two tick species, Dermacentor reticulatus and Rhipicephalus sanguineus, are supposed to transmit B. canis and B. vogeli respectively. In southern France, where dog infections with B. vogeli were recently confirmed, no comprehensive study was performed to date on piroplasm species infecting dogs. Thus, a large scale survey involving veterinary clinics, kennels and tick collection from the environment was conducted from 2010 to 2012 in this area.Results: From 2010 to 2012, 140 dog blood samples and 667 ticks were collected. All blood and a subset of ticks were screened for the presence of piroplasms by PCR amplification of 18S rDNA. B. vogeli, B. canis and T. annae were detected in 13.6, 12.9 and 0.7 % dogs respectively. B. vogeli and B. canis were detected in 10.5 % and in 1.6 % R. sanguineus ticks including 1.3 % co-infections. B. canis was the only species detected in D. reticulatus ticks (9.7 %). B. canis infections were only recorded in the southwest of France whereas B. vogeli was mainly found in the southeast. Finally, a significantly higher prevalence of B. vogeli infection was found in Gard compared to Corsica and Drme regions, both in dogs (p < 0.002) and R. sanguineus ticks (p < 0.02) although R. sanguineus was the main ticks species removed from dogs in those three areas.Conclusions: The survey confirmed the circulation of both B. canis and B. vogeli in dogs in southern France with differences in distribution probably linked to the distribution of their respective vectors. It also showed differences in prevalence of B. vogeli infection in areas similar in terms of risk of dogs infestation with R. sanguineus. Further studies focusing on genetic and microbiota of R. sanguineus ticks should be conducted to explore other biological interactions that may explain the differences observed.