Increasing temperatures due to climate change have contributed to a northward range expansion of Ixodes scapularis ticks in Canada. These ticks harbour pathogens of public and animal health significance, including Borrelia burgdorferi and Anaplasma phagocytophilum, which cause Lyme disease and anaplasmosis, respectively, in humans, dogs and horses, and Borrelia miyamotoi, which causes a flu-like relapsing fever in humans. To address the risks associated with these vector-borne zoonotic diseases, continuous tick surveillance is advised. This study examined spatial patterns of B. burgdorferi, B. miyamotoi and A. phagocytophilum from ticks submitted through a national study on ticks of companion animals. From 1 April 2019 to 31 March 2020, we received a total of 1541 eligible submissions from 94 veterinary clinics across Canada. Individual and pooled samples of a maximum of either 5 I. scapularis, I. pacificus or I. angustus samples from the same animal and of the same life stage were screened using real-time PCR targeting genes 23S rRNA for Borrelia spp. and msp2 for A. phagocytophilum. Confirmatory testing was conducted on all 23S rRNA positive samples using a duplex assay for ospA and flaB to differentiate B. burgdorferi and B. miyamotoi, respectively. Prevalence estimates were highest (>20%) for B. burgdorferi in southwestern Manitoba, eastern Ontario, southwestern Quebec, New Brunswick and Nova Scotia. Estimates of B. miyamotoi and A. phagocytophilum were much lower (<5%), except for higher A. phagocytophilum (>5%) estimates for southern Manitoba, eastern Ontario and Prince Edward Island. Findings from this study, combined with other surveillance approaches, can be used to guide veterinary and public health approaches for ticks and tick-borne diseases.