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A 12-year-old intact male Miniature Schnauzer dog with chronic diarrhea that was unresponsive to empirical treatment was presented to a referring veterinarian. A laparotomy was performed, and formalin-fixed biopsies of duodenum, jejunum, and colon were sent to Oklahoma Animal Disease Diagnostic Laboratory for evaluation. Histologic examination revealed a severe, diffuse, granulomatous enteritis and colitis with intralesional yeast and hyphal forms. Grocott methenamine silver stains revealed short, aseptate hyphae co-mingled with 2–8 µm, oval to round yeast organisms consistent with Histoplasma capsulatum. The atypical presentation of both yeast and hyphal forms prompted identification of the organism. Direct sequencing of a polymerase chain reaction product from paraffin-embedded intestinal samples confirmed the presence of Ajellomyces capsulatus with a homology over 99% to several sequences in GenBank. Ajellomyces capsulatus is the holomorphic name for H. capsulatum. Therefore, the mycelial form of a dimorphic fungus such as H. capsulatum can coexist with yeast cells within lesions of histoplasmosis. Following diagnosis, the dog was treated with itraconazole for 6 months and has improved. [ABSTRACT FROM PUBLISHER]