The genus Atoxoplasma (Garnham 1950) as a junior objective synonym of the genus Isospora (Schneider 1881) species infecting birds and resurrection of Cystoisospora (Frenkel 1977) as the correct genus for Isospora species infecting mammals.

Molecular and morphological data permit a rational subdivision of the paraphyletic Isospora into 2 apparently monophyletic groups of parasites, i.e., Isospora and Cystoisospora. Atoxoplasma was determined to be a junior objective synonym for Isospora. Tetrasporozoic, diplosporocystic oocysts possessing Stieda bodies in their sporocysts belong to Isospora (Eimeriidae) and have been described principally from the feces of birds. Tetrasporozoic, diplosporocystic oocysts without Stieda bodies in their sporocysts belong to Cystoisospora (Sarcocystidae).