The objective of our study was to survey Babesia infection rates by PCR and tick species on stray dogs to correlate the distribution of Babesia with the distribution of ticks infesting dogs in Taiwan. Three hundred eighty-eight blood samples and 3037 ticks were collected from 388 roaming, and free-ranging owned dogs at residential sites in Taiwan between January 2015 and December 2017. The prevalence of B. gibsoni and B. vogeli was 15.7% (61/388) and 9.5% (37/388), respectively. Most positive B. gibsoni dogs were found in the northern part of the country 56/61 (91.8%), whereas a few were found in the middle 5/61 (8.2%). Babesia vogeli infection rates were 10%, 3.6%, and 18.2% in the northern, central, and southern regions, respectively. Five species of ticks were found: Rhipicephalus sanguineus (throughout Taiwan), Rhipicephalus haemaphysaloides (in the north), Haemaphysalis hystricis (in the north and middle of Taiwan), and Amblyomma testidunarium and Ixodes ovatus (both in the north). None of the dogs in the south were infected with B gibsoni, which correlated with the absence of H. hystricis, a tick recently identified as the local vector for B gibsoni. Babesia vogeli was more equally distributed, coinciding with R. sanguineus, a tick that is present throughout Taiwan. Anaemia was detected in 86.9% of infected dogs; among these dogs, approximately 19.7% showed severe anaemia (HCT < 20). These findings provide useful advice for owners regarding outdoor activities with their dogs and local veterinarians with a regional differential diagnosis of babesiosis in Taiwan.