Chaetodon striatus is a cosmopolitan seawater species present in aquaria all over the world and its extractivism is quite high. The lack of studies on the reproductive biology of C. striatus contributes to the difficulty in managing the species outside its natural habitat. Without knowledge of the mechanisms that control or affect gonadal changes, reproduction of C. striatus in captivity has become almost impossible, considering that the species is quite sensitive and the effect of captive conditions on its reproductive biology is unknown. Therefore, this study aimed to evaluate the effect on its reproductive biology of the animal’s confinement and possible alteration in structure of the ovaries. In C. striatus, after oocyte development, for animals confined in small spaces, maturing oocytes undergo atresia. During atresia, ovarian follicles were at different stages of degeneration, characterized by the progressive loss of the basement membrane and disorganization of the follicle complex. In the advanced stage of follicular atresia, there was total loss of the basement membrane, culminating in degradation of the follicle complex. In unconfined animals, oocyte development and maturation were not affected. Confinement also affected the cell structure of the germinal epithelium, which showed large numbers of apoptotic bodies. The difference in cortisol and glucose levels between the unconfined and confined groups was significant, which may have to do with the change found in the ovaries, such as extensive follicular atresia and loss of the basement membrane.