The Eimeria lie within the family Eimeriidae.
Eimeria accounts for close to 75% of the species within this family, and it is the most specious of the genera of the Apicomplexa with 1,700 described species.

Attempts to subdivide this large taxonomic unit into separate genera have been made.
The classification of eimeriid coccidian was largely based on morphological and life cycle details.
More recently, classification has been done using rDNA and mitochondrial genes, which indicate Eimeria may be paraphyletic to Isospora and Cyclospora 
Eimeria: These species are tetrasporocystic with dizoic, nonbivalved sporocysts with or without Stieda bodies.
This new genus retains the majority of the species.

Goussia (Labbe 1896): These species are tetrasporocystic, dizoic, lack Stieda bodies, and have sporocyst walls consisting of two valves joined by a longitudinal suture.
This genus contains about 20 species.

Crystallospora (Thelohan 1893): The species in this genus is tetrasporocystic and dizoic, and have dodecahedral sporocysts composed of two hexagonal, pyrimidal valves joined at their bases by a suture.
This genus contains a single species, Crystallospora cristalloides
Epieimeria: The species in this genus are tetrasporocystic, dizoic, possess Stieda bodies, and undergo merogony and gametogony on the lumenal surface of the intestinal tract.
Three species are in this genus.
The Eimeria lie within the family Eimeriidae. Eimeria accounts for close to 75% of the species within this family, and it is the most specious of the genera of the Apicomplexa with 1,700 described species.
Attempts to subdivide this large taxonomic unit into separate genera have been made. The classification of eimeriid coccidian was largely based on morphological and life cycle details. More recently, classification has been done using rDNA and mitochondrial genes, which indicate Eimeria may be paraphyletic to Isospora and Cyclospora 
Eimeria: These species are tetrasporocystic with dizoic, nonbivalved sporocysts with or without Stieda bodies. This new genus retains the majority of the species.
Goussia (Labbe 1896): These species are tetrasporocystic, dizoic, lack Stieda bodies, and have sporocyst walls consisting of two valves joined by a longitudinal suture. This genus contains about 20 species.
Crystallospora (Thelohan 1893): The species in this genus is tetrasporocystic and dizoic, and have dodecahedral sporocysts composed of two hexagonal, pyrimidal valves joined at their bases by a suture. This genus contains a single species, Crystallospora cristalloides
Epieimeria: The species in this genus are tetrasporocystic, dizoic, possess Stieda bodies, and undergo merogony and gametogony on the lumenal surface of the intestinal tract. Three species are in this genus.
Eimeria