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The influence of habitat and associated prey assemblages on the prevalence of canine diseases in coyotes (Canis latrans) has received scant attention. From December 1997 through December 1999, we captured 67 coyotes in two ecologically distinct areas of Utah (USA): Deseret Land and Livestock Ranch and US Army Dugway Proving Ground. These areas differ in habitat and prey base. We collected blood samples and tested for evidence of various canine diseases. Prevalence of antibodies against canine parvovirus (CPV) was 100% in the Deseret population and 93% in the Dugway population. All juveniles in both populations had been exposed. We found no difference in the prevalence of antibodies against canine distemper virus (CDV) between the two populations (7% versus 12%; P=0.50). However, we did find an increase in antibodies with age in the Deseret population (P=0.03). Evidence of exposure to canine adenovirus (CAV) was found in both populations (52% and 72%; P=0.08). Prevalence of CAV antibodies was influenced by age on both areas (Deseret: P=0.003; Dugway: P=0.004). Antibodies to Francisella tularensis were low on both areas (2% and 4%). We found a significant difference (P=0.001) in the prevalence of exposure to Yersinia pestis between the two populations: 73% in Deseret compared to 11% in Dugway. This difference is most likely due to the prey species available in the two ecologically distinct study areas.