The 18S nuclear small subunit ribosomal RNA gene of piroplasms from wildlife and human cases of babesiosis in the western USA were isolated by PCR and sequenced. Phylogenetic analyses of these sequences and comparisons with sequences from other Babesia and Theileria species revealed that piroplasm isolates from the human cases were indistinguishable from some of the isolates from the western wildlife species, most notably the isolates from mule deer (Odocoileus hemionus). These results suggest that large ungulates may serve as reservoirs for human piroplasm infection. The western piroplasm isolates from humans and wildlife formed a distinct clade, separate from other piroplasms found worldwide.