Maximum parsimony phylogenetic reconstruction 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. Tree length was 3147 steps with a consistency index of 0.63 based on 927 parsimony-informative characters; percentage bootstrap support (500 replicates) is indicated at each node. The MP tree differed from the BI/ML tree only in the placement of E. meleagrimitis basal to a collection of lower intestinal tract parasites of chickens and turkeys. The MP analysis supported monophyly of the 5 Eimeria species of chickens that do not usually invade the cecal pouches.