Postmortem examination of a free-range white-tailed deer (Odocoileus virginianus) revealed severe emaciation, bilateral firm proliferation of the metatarsal diaphyses, and a large intrathoracic mass associated with the accessory lung lobe. Smaller masses were evident in the abomasum, duodenum, omentum, and the capsular surface of the liver. Microscopically, the masses were similar and were diagnosed as eosinophilic granulomas with intralesional fungal hyphae characteristic of Zygomycetes spp. Fungal hyphae were identified as Conidiobolus incongruus by 18S ribosomal RNA sequencing on fresh lung tissue. Furthermore, the proliferative lesions of the metatarsal bones along with the intrathoracic mass were compatible with hypertrophic osteopathy.