Fungal infections of the respiratory tract of horses are not as frequent as those of bacterial and viral origin, often leading to worsening of clinical conditions due to misdiagnosis and incorrect treatment. Coccidioidomycosis and histoplasmosis are systemic mycoses caused by the dimorphic fungi Coccidioides spp. and Histoplasma capsulatum, respectively, which affect humans and a variety of other animals, including equines. These systemic mycoses of chronic and progressive nature can exhibit clinical manifestations similar to other microbial infections. Thus, this article broadly discusses the epidemiology, etiology, virulence, pathogenesis, clinical presentation, treatment, and diagnostic strategies of coccidioidomycosis and histoplasmosis, to support accurate diagnosis.