Borrelia burgdorferi and Borrelia miyamotoi are tickborne zoonotic pathogens in Canada. Both bacteria are vectored by ticks, Ixodes scapularis in Atlantic Canada, but require wildlife reservoir species to maintain the bacteria for retransmission to future generations of ticks. Coyotes (Canis latrans) are opportunistic feeders, resulting in frequent contact with other animals and with ticks. Because coyotes are closely related to domestic dogs (Canis lupus familiaris), it is probable that coyote susceptibility to Borrelia infection is similar to that of dogs. We collected livers and kidneys of eastern coyotes from licensed harvesters in Nova Scotia, Canada, and tested them using nested PCR for the presence of B. burgdorferi, B. miyamotoi, and Dirofilaria immitis. Blood obtained from coyote livers was also tested serologically for antibodies to B. burgdorferi, Ehrlichia canis, Anaplasma phagocytophylum, and D. immitis. Borrelia burgdorferi and D. immitis were detected by both nested PCR and serology tests. Seroreactivity to A. phagocytophylum was also found. Borrelia miyamotoi and E. canis were not detected. Our results show that coyotes in Nova Scotia have been exposed to a number of vectorborne pathogens.