A 7-yr-old male Malayan flying fox (Pteropus vampyrus) presented with chronic, recurrent bilateral conjunctivitis and palpebral chemosis. Variable, temporary response to topical ocular antibiotic-corticosteroid therapy occurred. Histopathology of a conjunctival biopsy was consistent with allergic conjunctivitis. The bat was treated systemically with antihistamines and topically with an ocular antibiotic-corticosteroid combination for acute episodes of conjunctivitis. Pruritus, severe alopecia of the head and neck, and moist dermatitis later developed in conjunction with bilateral conjunctivitis. Cytology and histopathology of affected skin supported a diagnosis of atopic dermatitis. Although the assay was not validated for P. vampyrus, serum immunoglobulin E levels against multiple possible antigens were measured. Acceptable resolution of clinical signs was achieved for 20 mo following systemic cyclosporine administration. Cyclosporine levels were measured in whole blood for additional therapeutic monitoring. This is the first reported case of histopathologic support for atopic dermatitis, novel diagnostics, and palliative management of atopy using cyclosporine in a flying fox.