The morphology of organisms reflects a balance between their evolutionary history, functional demands, and biomechanical constraints imposed by the immediate environment. In many fish species, a marked shift in the selection regime is evident when pelagic larvae, which swim and feed in the open ocean, settle in their adult benthic habitat. This shift is particularly dramatic in coral-reef fishes, where the adult habitat is immensely complex. However, whether the adult trophic ecotype affects the morphology of early life stages is unclear. We measured a suite of 26 functional-morphological traits in the head and body of larvae from an ontogenetic series of 16 labrid species. Using phylogenetic comparative methods, we reconstructed the location of adaptive peaks of larvae whose adults are associated with different trophic ecotypes. We found that the morphospace occupation in these larvae is largely driven by divergent adaptations to the adult benthic habitats. The disparity between adaptive peaks is achieved early and does not monotonically increase with size. Our findings refute the notion that larvae rapidly acquire the trophic-specific traits during a metamorphic period immediately prior to settlement. This early specialization might be due to the highly complex musculoskeletal system of the head that cannot be rapidly modified.