Abstract: Using the method of random amplified polymorphic DNA (RAPD)and three primers,we got the sequences of the first internal transcribed spacer region (ITS1) and a small subunit of rRNA (SSrRNA),and then constructed phylogenetic trees of some genera/species in peritrichs.A comparison of the tree structures showed that SSrRNA was more reliable marker for analyzing the phylogenetic position of peritrichs within Ciliophora.The phylogenetic tree based on the SSrDNA sequence strongly supported the monophyly of the subclass Peritrichia,or its subclass rank is reasonable.In addition,there are some evidences showing that peritrichs are a higher group in Oligohymenophoreans.