The small subunit ribosomal RNA (16S-like rRNA) coding regions of the hypotrichous ciliates Onychodromus quadricornutus and Oxytricha granulifera were amplified using polymerase chain reaction techniques. Complete sequences were determined for the amplified genes and compared to those of other ciliated protozoa. In phylogenetic trees inferred using distance matrix methods oxytrichids are not seen as a cohesive phylogenetic group. Oxytricha nova is most closely related to Stylonychia pustulata in a lineage that also includes O. quadricornutus. This phylogeny contradicts phylogenetic schemes in which Onychodromus is considered to be a primitive hypotrichous ciliate and suggests that O. nova was misidentified as members of the genus Oxytricha.