Trypanosoma cruzi is a vector-borne, protozoal parasite of mammals. Infected humans, dogs (Canis lupus familiaris), and nonhuman primates may remain asymptomatic or may develop Chagas disease, most commonly characterized by lymphoplasmacytic myocarditis with myocardial degeneration and fibrosis, ultimately resulting in heart failure. Although wildlife species have important roles as sylvatic reservoirs, investigations into the pathology of T. cruzi in wildlife are limited to a few studies documenting histologic lesions in opossums (Didelphis spp.) and raccoons (Procyon lotor). Pathology in coyotes (Canis latrans) has not, to our knowledge, been described, despite their recognition as a reservoir and close genetic relationship to domestic dogs. Our objectives were to perform a detailed, comparative cardiac pathology study of sympatric, naturally infected coyotes and raccoons, to characterize the overall T. cruzi infection prevalence in the heart and blood of each species via PCR, and to identify infecting discrete typing units (DTUs). We sampled hunter-harvested coyotes (n=120) and raccoons (n=24) in a 28 county region of central and south Texas, US. Raccoons were significantly more likely to have positive PCR results (P<0.001) with a prevalence of 62% (15/24), comprising DTU TcIV exclusively, with mild to no evidence of cardiac pathology. In contrast, coyotes had a lower infection prevalence (8%, 10/120), comprising DTU TcI exclusively, with lymphoplasmacytic myocarditis observed in four of the six PCR-positive animals. Many raccoons had PCR-positive blood and heart tissue simultaneously, supporting previous reports that raccoons maintain parasitemia into chronic stages of infection; in contrast, none of the PCR-positive coyotes were positive in both heart and blood. Our findings demonstrate marked differences in T. cruzi infection dynamics between coyotes and raccoons, with important implications for reservoir potential and their role in transmission cycles.