The small subunit ribosomal RNA (eukaryotic 16S rRNA) gene from Giardia trophozoites, isolated from 8 different prairie voles and 8 different muskrats, was amplified by the polymerase chain reaction. The 16S rDNA was sequenced in its entirety for 2 prairie vole and 2 muskrat Giardia. In addition, the 5' 500 nucleotides of the 16S rDNA from Giardia isolates from each of 6 voles and 6 muskrats were amplified and sequenced. The results show that Giardia from voles and muskrats are very similar to each other but differ substantially from Giardia isolated from humans. We believe that the Giardia isolate from voles and muskrats constitutes a distinct species, which will be referred to as Giardia microti. These results suggest that both voles and muskrats are parasitized by the same species of Giardia, that this species is different from the Giardia that parasitizes humans, and that voles and muskrats do not contribute to the zoonotic character of human giardiasis.