Coral reefs represent the most biologically diverse marine ecosystem, however, they are vulnerable to environmental changes and impacts. Therefore, information on the variability of environment and biodiversity is essential for the conservation management of coral reefs. In this study, a soundscape analysis based on range-wide and long-term underwater recording were conducted. Maps of damselfishes and snapping sounds could be obtained by supervised feature extraction of species specific sounds. Using unsupervised classifier, Shannon index of soundscape diversity was shown to be high in deep waters. Mesophotic coral reefs in deep water have been considered as potential refuges for symbiotic corals when coral bleaching happens in shallow reefs due to high sea surface temperature. Results seemed to be consistent with this hypothesis.