Anglerfishes (Lophiiformes) have evolved diverse morphological solutions for life in the deep sea (>200 m). Previous studies have shown that the bathypelagic lineage (Ceratioidei) exhibits high evolutionary rates; however, the intrinsic mechanisms underlying this accelerated evolution remained unclear. Here, we examine patterns of modularity and integration, rates of morphological evolution, and evolutionary rate matrices across the skulls of 100 anglerfish species spanning shallow and deep-sea habitats using geometric morphometrics and phylogenetic comparative methods. We find that both deep-benthic and bathypelagic anglerfishes exhibit stronger patterns of integration compared to their shallow-water relatives. The iconic bathypelagic anglerfishes (Ceratioidei) differ from other Lophiiformes by exhibiting an integrated upper-lower jaw system, likely driven by selection for feeding efficiency in resource-scarce environments. Jaw evolution in Ceratioidei, Chaunacoidei, and Ogcocephaloidei exhibits novel evolutionary trajectories that differ from the dominant pattern across Lophiiformes. Our findings suggest that extreme environments promoted morphological innovation in anglerfishes through evolution in novel phenotypic directions and strengthening of evolutionary integration.