A cladistic analysis of 23 extant species of the deep-sea pedunculate cirripede family Scalpellidae was undertaken, based on 61 shell plate characters, and taking the Jurassic-Cretaceous scalpellomorph genus C retiscalpellum as an out-group. The consensus tree shows progressive morphological change from basal to more derived taxa, but a derived group is marked by major morphological innovation, including 27 character state changes that permit subdivision of the family into two sharply demarcated clades - the more basal group is here placed within a redefined Scalpellinae (A rcoscalpellum, A rcuatoscalpellum gen. nov., D iotascalpellum gen. nov., G raviscalpellum, R egioscalpellum gen. nov., and S calpellum), and a more derived group named A migdoscalpellinae subfam. nov. that shows numerous progressive trends in morphology, permitting the recognition of three genera (A migdoscalpellum, C atherinum, and W eltnerium). The phylogeny is independently supported by a recently published multiple DNA marker-based molecular phylogeny. The more basal Scalpellinae appeared in the Aptian (Early Cretaceous, 120 Mya), and derived Amigdoscalpellinae were already present by the Campanian (Late Cretaceous, 78 Mya), represented by C atherinum anglicum sp. nov. and A migdoscalpellum bellulum from the UK Chalk. Specialized receptacles to accommodate dwarf males in the apical interior of the scutum evolved at least three times during the history of the scalpellids. © 2015 The Linnean Society of London.