Reptiles are the animals with the most described coccidian species among all vertebrates. However, the co‐evolutionary relationships in this host–parasite system have been scarcely studied. Paperna & Landsberg (South African Journal of Zoology, 24, 1989, 345) proposed the independent evolutionary origin of the Eimeria‐like species isolated from reptiles based on morphological and developmental characteristics of their oocysts. Accordingly, they suggested the reclassification of these parasites in two new genera, Choleoeimeria and Acroeimeria. The validity of the genera proposed to classify reptilian Eimeria species remained unresolved due to the lack of species genetically characterized. In this study, we included 18S rRNA gene sequences from seven Eimeria‐like species isolated from five different lizard host families. The phylogenetic analyses confirmed the independent evolutionary origin of the Eimeria‐like species infecting lizards. Within this group, most species were placed into two monophyletic clades. One of them included the species with ellipsoidal oocysts (i.e. Choleoeimeria‐like oocysts), whereas the species with more spheroidal oocysts (i.e. Acroeimeria‐like oocysts) were included in the second one. This result supports the taxonomic validity of the genera Acroeimeria and Choleoeimeria.