DNA barcoding identifies Eimeria species and contributes to the phylogenetics of coccidian parasites (Eimeriorina, Apicomplexa, Alveolata)

► Cytochrome c oxidase subunit I (COI) sequences obtained from coccidia. ► COI sequences are useful DNA barcode targets for Apicomplexa. ► COI sequences are better than nuclear 18S rDNA sequences for species delimitation. ► Character-based phylogenetic analysis extends COI sequence utility beyond DNA barcoding for species identifications.