Bayesian inference and maximum likelihood phylogenetic reconstructions using mitochondrial genome sequences of 16 Eimeria species. The analyses included 5 species infecting turkeys and 7 species infecting chickens and used Eimeria magna (a parasite of rabbits) as the functional outgroup to root the tree. Node support is indicated for BI (posterior probability, first number) and for ML (% bootstrap, second number) for all nodes with greater than 0.5 posterior probability. Neither the Eimeria species infecting chickens nor the Eimeria species infecting turkeys formed monophyletic groups. Both the BI and ML analyses supported monophyly of the 5 Eimeria species of chickens that do not usually invade the cecal pouches but branching order among these parasites was poorly resolved in both.