From a practical point of view, the determination of species in the wild is based on their phenotypes. Consequently, many species remain unknown because they are visually indistinguishable from described species. Although molecular methods and advances in bioacoustical analysis have been extensively used to uncover cryptic species, the combination of both methodologies is still rare and concerns only some terrestrial taxa such as insects, bats, frogs and birds. In this study, we aim to determine whether the sounds produced by different populations of fish can also be a tool to distinguish and identify cryptic species. The humbug damselfish complex, Dascyllus aruanus, is widely distributed across the Indo-Pacific Ocean and, since 2019, is thought to be composed of at least two species with Dascyllus aruanus in the Pacific Ocean and Dascyllus abudafur in the Indian Ocean. Recordings were made over a large geographical area with populations from Madagascar (Indian Ocean), Taiwan (Pacific Ocean) and French Polynesia (Society Islands). Two kinds of sounds were used for analysis: sounds associated with conspecific chases, and sounds produced during the “signal jump” of courtship behaviour. The sounds associated with signal jumps differ geographically. Acoustic feature differences between Taiwan and Madagascar align with the existence of genetic differences confirming specific status and supporting for the first time that sounds can help to discriminate cryptic species in Teleosts. However, differences in both acoustic features and genetic data can also be found between Taiwan and French Polynesia suggesting two clearly distinct populations. Using the same reasoning, we propose to resurrect the epithet “emamo” (Lesson 1830) for the Society Island humbug damselfish. Interestingly, sounds associated to conspecific chases are more variable than sounds related to signal jumps, suggesting that there are more constraints on sounds related to courtship since they would serve as indicators for species identity and contribute to premating isolation.