Eimeria arizonensis, E. albigulae and E. onychomysis, morphologically similar species from closely related murid rodents,
were distinguished using nuclear rDNA ITS1 sequences obtained from multiple isolates of each taxon. ITS1 sequences
were also obtained from 6 other species parasitizing murid rodents: E. falciformis, E. langebarteli, E. nieschulzi, E. papillata,
E. separata and E. sevilletensis, and from E. reedi, a parasite of heteromyid rodents. Under parsimony and maximum
likelihood analyses, the isolates of E. arizonensis, E. albigulae and E. onychomysis were differentiated as closely related,
monophyletic lineages. Maximum likelihood pairwise distances between the latter species ranged from 7 to 12%, and
distances within each species ranged from <1 to 5%; thus it is suggested that ITS1 genetic distances may be used to
facilitate taxonomic differentiation of Eimeria spp. Against expectation, phylogenetic procedures placed E. reedi within the
phylogeny of the Eimeria of murid rodents. ITS1 sequencing appears to provide data that can be used for taxonomic and
phylogenetic studies on the speciose genus Eimeria, and may be especially useful when samples contain insufficient
numbers of oocysts for other molecular-based methods, e.g. RAPD–PCR.