Between June 2016 and June 2019, we surveyed 62 Mediterranean geckos, Hemidactylus turcicus, from Abu Rawash, Giza, Egypt, for the presence of endoparasites. In June 2016, we found 3 individuals to be infected with Eimeria lineri. We studied the morphology and inner structures of its sporulated oocysts, and the locations of its intestinal endogenous stages. We also extracted genomic DNA from these sporulated oocysts and successfully sequenced a 632-bp fragment of the 18S rRNA gene. Phylogenetic analyses using this partial sequence allowed us to support previous studies that assigned E. lineri to the genus Acroeimeria. Our consensus sequence was used to query similar 18S rDNA sequences from GenBank, and 14 sequences were selected. The phylogenetic analysis inferred by maximum likelihood and Bayesian inference methods gave similar results, as both separated the sequences into 2 clades: (1) a monophyletic group of Goussia species (from fish); and (2) a strongly supported clade that separated 4 Choleoeimeria species from a polyphyletic group of species that clustered A. lineri with 3 other Acroeimeria species and 3 Eimeria species from lizards, including Eimeria tiliquae from Tiliqua rugosa (Gray, 1825), Eimeria tokayae from Gecko gecko (L., 1758), and Eimeria eutropidis from Eutropis macularia (Blyth, 1853). Our study supports the placement of E. lineri into the Acroeimeria and contributes additional life history information toward understanding the evolutionary origin of the Eimeria-like species that have sporocysts without Stieda bodies in their oocysts and that infect saurian reptiles. We also support the concept that several traits (morphological, endogenous, and gene sequences) are both necessary and important for authors to include when making generic reassignments within the eimeriid coccidia.