Within the neotropical bat family Phyllostomidae, species of the subfamilies Glossophaginae and Lonchophyllinae have many derived traits adapted to nectarivory, including elongated snouts and jaws and the ability to perform hovering flight. We compared patterns of cranial variation within and between these groups with respect to within-group allometric trajectories, based on 19 linear morphometric variables collected from 221 specimens representing all genera and 62% of the species in the two subfamilies. In a pooled principal component analysis, species belonging to Lonchophyllinae and Glossophaginae occupy similar regions in morphospace, though the latter species have a greater variance. Principal components and common principal components analyses for separate taxonomic lineages (subfamilies, tribes and subtribes) revealed distinct static allometric trajectories among these groups, with variables associated with elongation of the rostrum having distinct allometric coefficients. Our results indicate that distinct cranial morphotypes associated with the degree of elongation of the rostrum in phyllostomid nectarivores are allometrically characteristic of each lineage. The patterns suggest that cranial integration in phyllostomid nectarivores reflects primarily their phylogenetic history rather than adaptive pressures resulting from specialization to particular feeding resources.