An adult male Ruwenzori long-haired fruit bat (Rousettus lanosus) presented for lethargy and unthriftiness. Physical examination revealed cranial alopecia, mandibular ulceration, and dehydration. Supportive care and antibiotic therapy were initiated. The bat was found dead 3 days after presentation. Necropsy revealed alopecia on the head and body, exposed dried bone on the rostral tip of the mandible, and excessive clear pleural fluid. Lungs were congested and contained miliary white foci disseminated randomly throughout the parenchyma. Subcutaneous, intra-thoracic, and intra-abdominal adipose depots were minimal. Histologic examination of skin and lung revealed the presence of algal-like organisms morphologically consistent with Prototheca spp. Polymerase chain reaction amplification revealed >99% sequence identity match with Prototheca zopfii. Protothecosis has been previously reported in a single bat, Lyle's flying fox (Pteropus lylei), in Switzerland, but definitive protothecal speciation was not possible.