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.