Evidence from the wild as to the ecological and evolutionary consequences of top predator depletions remains limited, especially in marine systems. Given the pace and extent of predator loss, an understanding of these processes is important. Two sets of adjacent coral reef systems off north-Western Australia have similar biological, physical and environmental conditions, but one of the reef systems has been exposed to nearly exclusive commercial fishing of sharks. Across reefs where sharks have been depleted, prey fishes had significantly smaller caudal fins and eyes compared to the reefs with intact shark populations (up to 40 and 46% relative difference in standardized means). These patterns were consistent across 7 teleost prey species (N = 611 individuals) that vary in behavior, diet and trophic guild. We hypothesize that these morphological patterns were primarily driven by differences in shark predation. Morphological differences were not consistent with plausible alternative explanations (habitat complexity, temperature, light, current, food availability, prey targets, competition) as primary drivers. These results provide field evidence of morphological changes in prey potentially due to predator depletions consistent with ecological predictions; specifically, predator loss caused a reduction in the size of prey morphological traits associated with predator detection and evasion. While our analysis cannot differentiate between rapid evolutionary change versus morphological plasticity due to shark depletions, either possible outcome would indicate that predator removals may have profound effects on body shapes of prey communities. This is particularly significant in the case of sharks, given that the consequences of their widespread removal have been a topic of significant speculation, debate and concern.