A phylogenetic hypothesis was constructed with the use of ssu rDNA sequence data from 27 eugregarine species parasitizing a variety of arthropod hosts and habitats. The data were used to address higher-level character transitions, identify clades, recognize supraspecific taxonomic groups, assess the existing gregarine classification, and assess the effects of host metabolic pattern and habitat transitions on the radiation of the septatorinid gregarines. Suprageneric character transitions for association form, association timing, syzygy, gametocyst dehiscence, and oocyst liberation are defined. New character search based on the proposed phylogeny produced a morphological character set that correlates strongly with the sequence data. These morphological character sets are mapped to the new septatorinid phylogeny. Existing superfamily groups within Septatorina were recovered and a new superfamily recognized. At the family level, the monophyly of Actinocephalidae and Stylocephalidae is confirmed and the polyphyly of Gregarinidae is partially resolved with the recognition of Blabericolidae. At the generic level, the monophyly of Protomagalhaensia and Xiphocephalus is confirmed, the polyphyly of Leidyana is partially resolved with the recognition of Blabericola, and the polyphyly of Gregarina is revealed but cannot be resolved without additional taxonomic data. High-level diversification of Septatorina resulted from adaptations of the gametocyst, allowing colonization of both terrestrial and sweet-water habitats. Major radiations within the group correlate with host metamorphic pattern, suggesting that evolutionarily, gregarine species track niche resources along lines of transmission; they do not necessarily track host species in evolutionary time. Gregarine assemblages within a single host species may be either vicariant assemblages, (i.e., products of coevolutionary, phylogenetic effects), or ecotypic assemblages, (i.e., products of ecological fitting and host switching). The following systematic or nomenclatural acts are committed. Stenophoroidea and Gregarinoidea are emended. Diagnoses of Stenophoroidea, Gregarinoidea, and Sphaerocystidae are revised. Stylocephaloidea n. supfam., Blabericolidae n. fam., and Blabericola n. gen. are recognized and erected. Blabericola princisi n. comb., Blabericola cubensis n. comb., Blabericola haasi n. comb., and Blabericola migrator n. comb. are recognized. Schneideria, Neoschneideria, and Paraschneideria are removed from Sphaerocystidae and placed in Actinocephalidae. Protomagalhaensia is removed from Hirmocystidae and placed in Blabericolidae. Pyxinia is removed from Stylocephaloidea: Actinocephalidae and placed in Stenophoroidea: Monoductidae.
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