Fisheries management now extends from the stock to the ecosystem. The foundation for fisheries management on an ecosystem basis must lie in appropriate modelling of the ecosystems. A prerequisite for such models requires data on the two interactive components of the ecosystem: the biotope (physical environment), and the community of living species. In this context, acoustics become essential, as this tool can provide qualitative and quantitative data on various communities of species, and furthermore allows the seldom-attainable study of their interactions. In fact, acoustics allow the monitoring of entire communities, from plankton to large predators, as well as certain aspects of the physical environment, such as substratum characteristics. Acoustics have been used during the last two decades mainly to provide fishery-independent estimates of stocks. The intention of this paper is to promote the use of acoustics for studying marine ecosystems and to encourage the emergence of new generations of ecosystem models. As an example of integrative research based on acoustic data, we will present the approach and the results of a scientific programme (ECOTAP) carried out to study the tuna pelagic ecosystem in French Polynesia. We then discuss the use of acoustics as a tool for ecosystem-based studies and management.