The demand that anatomical structures work together to perform biological functions is thought to impose strong limits on morphological evolution. Breakthroughs in diversification can occur, however, when functional integration among structures is relaxed. Although such transitions are expected to generate variation in morphological diversification across the tree of life, empirical tests of this hypothesis are rare. Here we show that transitions between suction-based and biting modes of prey capture, which require different degrees of coordination among skull components, are associated with shifts in the pattern of skull diversification in eels (Anguilliformes). Biting eels have experienced greater independence of the jaws, hyoid and operculum during evolution and exhibit more varied morphologies than closely related suction feeders, and this pattern reflects the weakened functional integration among skull components required for biting. Our results suggest that behavioural transitions can change the evolutionary potential of the vertebrate skeleton by altering functional relationships among structures.