Respiratory disease is common in dolphins, primarily affecting pulmonary parenchyma and sparing large airways. Over a 10-year period, 4 captive adult bottlenose dolphins succumbed to chronic, progressive respiratory disease with atypical recurrent upper respiratory signs. All dolphins had severe, segmental to circumferential fibrosing tracheitis that decreased luminal diameter. Histologically, tracheal cartilage, submucosa, and mucosa were distorted and replaced by extensive fibrosis and pyogranulomatous inflammation centered on fungal hyphae. In 3 of 4 cases, hyphae were morphologically compatible with Aspergillus spp and confirmed by culture in 2 cases. Amplification of fungal DNA from tracheal tissue was successful in one case, and sequences had approximately 98% homology to Aspergillus fumigatus. The remaining case had fungi compatible with zygomycetes; however, culture and polymerase chain reaction were unsuccessful. Lesions were evaluated immunohistochemically using antibodies specific to Aspergillus spp. Aspergillus-like hyphae labeled positively, while presumed zygomycetes did not. These cases represent a novel manifestation of respiratory mycoses in bottlenose dolphins.