AbstractCnidae are complex intracellular capsules made by all cnidarians. The most diverse of these capsules are nematocysts, which are made by all members of the phylum; spirocysts and ptychocysts are made only by members of some lineages, and they show less functional and structural diversity. In nematocysts, the apex has been shown to be either a hinged cap (operculum) or three flaps that flex outward during discharge. The operculum is known only from medusozoan nematocysts; flaps are known only from nematocysts of members of the hexacorallian order Actiniaria, although they have been inferred to be characteristic of Anthozoa, the group to which Actiniaria belongs. Using scanning and transmission electron microscopy, we discover a third apical morphology in nematocysts, an apical cap, which we find in all nonactiniarian anthozoans examined. This apical cap is identical structurally to the apical cap of spirocysts, and it resembles the apical structure of ptychocysts, whose apex is documented here for the first time. Additionally, a full survey of nematocysts from all body structures of two actiniarians demonstrates that a particular type of nematocyst, the microbasic p‐mastigophore of the mesenterial filaments, does not have apical flaps. The observed variation does not correspond to conventional categorization of capsule morphology and raises questions about the function and structure of capsules across Cnidaria. Despite some ambiguity in optimization of ancestral states across cnidae, we determine that the apical cap is the plesiomorphic structure for anthozoan cnidae and that apical flaps are a synapomorphy of Actiniaria. At present, the operculum is interpreted as a synapomorphy for Medusozoa, but either it or an apical cap is the ancestral state for nematocysts. J. Morphol. 273:121–136, 2011. © 2011 Wiley Periodicals, Inc.