Brains are very plastic, both in response to phenotypic diversity and to larger evolutionary trends. Differences between taxa cannot be easily attributed to either factors. Comparative morphological data on higher taxonomic levels are scarce, especially in ray-finned fishes. Here we show the great diversity of brain areas of more than 150 species of ray-finned fishes by volumetric measurements using block-face imaging. We found that differences among families or orders are more likely due to environmental needs than to systematic position. Most notable changes are present in the brain areas processing sensory input (chemosenses and lateral line vs. visual system) between salt- and freshwater species due to fundamental differences in habitat properties. Further, some patterns of brain volumetry are linked to characteristics of body morphology. There is a positive correlation between cerebellum size and body depth, as well as the presence of a swim bladder. Since body morphology is linked to ecotypes and habitat selection, a complex character space of brain and body morphology and ecological factors together could explain better the differentiation of species into their ecological niches and may lead to a better understanding of how animals adapt to their environment.