Bottlenose dolphins (Tursiops truncatus) are one of the most popular dolphin species housed in aquaria in Japan. Previous studies have demonstrated that respiratory infections, mainly caused by bacteria and occasionally fungi, are one of the most common diseases in this species. Both Candida spp. and Aspergillus spp. are the most important species as the cause of respiratory fungal infections for this species in Japan. Since these fungi are ubiquitous in the environment surrounding dolphins and aquaria, and the spores may scatter easily in their habitats (poolside), it is very difficult to remove these fungi from their habitats. Therefore, in aquaria in Japan, preventing respiratory fungal infections and treating these infections appropriately in this species including in pregnant and lactating animals and their calves are necessary to maintain the health and number of the current population; this approach must also be applied for respiratory bacterial infections. In this review, to gain a better understanding regarding respiratory fungal infections in this species, the current status of these infections and results of clinical studies in the Port of Nagoya Public Aquarium (PNPA) are described. Moreover, future issues that have been revealed as a result of treating these infections in this species including in pregnant and lactating animals and their calves in the PNPA and that need to be solved are described.