There are numerous species of apicomplexans that infect poikilothermic vertebrates, such as fishes, and possess unique morphological features that provide insight into the evolution of this important phylum of parasites. Here, the relationship of the fish-infecting Calyptospora species to other coccidians was investigated based on DNA sequence analysis. Genetic data from the small subunit ribosomal DNA region of the genome were obtained for three of the five nominal species in the genus Calyptospora. Phylogenetic analyses supported a monophyletic lineage sister to a group composed of mostly Eimeria species. The monophyly of Calyptospora species supports the validity of the family Calyptosporidae, but the sister relationship to Eimeria species might also suggest the Eimeriidae be expanded to encompass Calyptospora. The validity of the family Calyptosporidae has been questioned because it is delineated from the Eimeriidae largely based on life cycle characteristics and sporocyst morphology. In general, Eimeria species have a homoxenous life cycle, whereas the type species of Calyptospora is heteroxenous. In the absence of experimental transmission studies, it may be difficult to demonstrate whether all Calyptospora species are heteroxenous. Other distinct morphological characteristics of Calyptospora such as an incomplete sporocyst suture, an apical opening for sporozoite release, a thin veil surrounding sporocysts supported by sporopodia, and a lack of Stieda and sub-Stieda bodies suggest there may be adequate features to delineate these taxa. Even without life cycle data for all species, the morphology and genetic data provide a means to reliably classify Calyptospora species. Placement in either the Calyptosporidae or Eimeriidae is discussed, along with issues relating to the phylogeny of the genus Goussia.