Abstract: ISSR analysis was conducted to investigatethe genetic relationships of five ciliate strains: Epistylisplicatilis, Parame-cium bursaria, Stentor polymorphus, Tetrahymena thermophila BF1 and T. thermophila BF5. Out of 13 ISSR primers, 6 primersgenerated highly reproducible and polymorphic DNA fragments. The genetic trees were constructed based on ISSR amplificationfingerprintings using both unweighted pair -group method for arithmetic averages analysis (UPGMA) and neighbor -joining ( NJ)methods. Two T. thermophila strains formed one branch first. E. plicatilis clustered with S. polymorphus, then grouped withT. thermophila. P. bursaria formed a separate branch. This shows that ① the peritrichs may be recognized as the particularciliates within Oligohymenophorea, and they should be elevated to a higher taxonomic rank; ② the Peritrichia E. plicatilis hasthe closer relation with theHymenostomatia T. thermophila than the Peniculia P. bursaria, which is the primordial group in theclassOligohymenophorea;③ The genome of the five ciliate strains contain these microsatellite DNA sequences: ( GTG)4,(GACA)4, (AG)8, ( CAA)6and (GAA)6.