Key morphological traits reveal changes in functional morphospace occupation of reef fish assemblages over time. We used measurements of key functional attributes (i.e., lower jaw length and orbit diameter) of 208 fossil fish species from five geological periods to create bivariate plots of functional morphological traits through time. These plots were used to examine possible function and ecological characteristics of fossil reef fish assemblages throughout the Mesozoic and Cenozoic. A previously unknown trend of increasing orbit diameter over time became apparent. The Teleostei are the principal drivers of this change. The Eocene appears to mark a dramatic increase in two previously rare feeding modes in fishes: nocturnal feeding and high-precision benthic feeding. Interestingly, members of the Pycnodontiformes had relatively large eyes since the Triassic and appear to be the ecological precursors of their later teleost counterparts and may have been among the earliest nocturnal feeding fishes. Our results highlight potential changes in the roles of fishes on coral reefs through time.