Seven Euplotes spp. were investigated using amplified ribosomal DNA restriction analysis (RFLP, riboprinting). This involved the use of the polymerase chain reaction (PCR) to amplify a segment of the ciliate genome, followed by restriction digestion to yield restriction fragment length polymorphisms among the seven euplotids. Distinctly different restriction digestion haplotypes and similarity indices among the seven species (0.15–0.78) were obtained, which were used to separate the seven species and construct a distance tree among them. Seven species were separated into three clusters: i.e. E. rariseta, E. eurystomus–E. woodruffi–E. octocarinatus–E. charon and E. minuta–E. vannus. The present investigation demonstrates that RFLP riboprinting is a useful technique for species separation. Some limitations of this method for inferring the relationships above species level are discussed.