Climate change has had a significant impact on many marine organisms. To investigate the effects of environmental changes on deep-water benthic fishes, we selected the genus Oplegnathus and applied species distribution modeling and ecological niche modeling. From the last glacial maximum to the present, the three Oplegnathus species (O. conwayi, O. robinsoni, and O. peaolopesi) distributed in the Cape of Good Hope region of southern Africa experienced fitness zone fluctuations of 39.9%, 13%, and 5.7%, respectively. In contrast, O. fasciatus and O. punctatus, which were primarily distributed in the western Pacific Ocean, had fitness zone fluctuations of −6.5% and 11.7%, respectively. Neither the O. insignis nor the O. woodward varied by more than 5% over the period. Under future environmental conditions, the range of variation in fitness zones for the three southern African Oplegnathus species was expected to be between −30.8% and −26.5%, while the range of variation in fitness zones for the two western Pacific stonefish species was expected to remain below 13%. In addition, the range of variation in the fitness zones of the O. insignis was projected to be between −2.3% and 7.1%, and the range of variation in the fitness zones of the O. woodward is projected to be between −5.7% and −2%. The results indicated that O. fasciatus and O. punctatus had a wide distribution and high expansion potential, while Oplegnathus species might have originated in western Pacific waters. Our results showed that benthic fishes were highly adaptable to extreme environments, such as the last glacial maximum. The high ecological niche overlap between Oplegnathus species in the same region suggested that they competed with each other. Future research could explore the impacts of environmental change on marine organisms and make conservation and management recommendations.