The development of the self-contained underwater breathing apparatus (scuba) in the mid-twentieth century provided ecologists with unprecedented access to reef fishes and their ecosystems. These studies fostered major advances in our understanding of tropical and temperate reef fishes through comparisons of disparate systems to identify common ecological and evolutionary threads, and through the integration of processes across multiple levels of biological organization. For each of these levels (individuals, populations, communities, and entire ecosystems) we describe the diversity of research approaches enabled by scuba, the insights they generated, and the resulting conceptual contributions to ecology and evolution. Much of the research described here has direct and valuable application to management and policy decisions for fisheries and conservation of reef species and ecosystems.