ISSR analysis was conducted to investigate the genctic relationships of five ciliate strains: Epistylis plicatilis, Paramecium bursaria, Stentor polymorphus, Tetrahymena thermophila BF1 and T. thermophila BF5. Out of 13 ISSR primers, 6 primers generated highly reproducible and polymorphic DNA fragments. The genetic trees were constructed based on ISSR amplification fingerprintings 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 with T. thermophila. P. bursaria formed a separate branch. This shows that (1) the peritrichs may he recognized as the particular ciliates within Oligohymenophorea, and they should be elevaled to a higher taxonomic rank; (2) the Peritrichia E. plicatilis has the closer relation with the Hymenostomatia T. thermophila than the Peniculia P. bursaria, which is the primordial group in the class Oligohymenophorea; (3) The genome of the five ciliate strains contain these microsatellite DNA sequences: (GTC)(4), (GACA)(4), (AG)(8), (CAA)(6) and (GAA)(6).