We describe a case of canine mycoses initially diagnosed by clinical signs and enzyme-linked immunosorbent assay anti-fungal test, and later confirmed by the isolation of Paecilomyces sp. during the post-mortem examination. The fungus was isolated from lesions in the kidneys, mitral valve, abdominal aorta and vertebral discs. In this kind of process, it is important to identify the responsible agent early in order to make a study of anti-fungal susceptibility and establish effective treatment.