Peritrichous ciliates have been known for more than 300 years as a distinct group, but there is as yet no firm conclusion on their phylogenetic position among the ciliates and the phylogenetic relationships among peritrichs. SSrRNA gene sequences were chosen as molecular marker to study the phylogeny of peritrichs in this dissertation based on devising the method in situ (field-sampled species for PCR) and analyzing three molecular markers (RAPD, ITS1 and SSrRNA gene sequences). Firstly, SSrDNA complete sequences of 13 species of peritrichs (6 families, 8 genera) were sequenced. Then, the maximum parsimony and neighbor-joining phylogentic trees were constructed. Lastly, based on analysis on phylogentic relationships among 39 ciliates combined with their main morphologic characters, some conclusion were drawn: 1) the monophyly of the peritrichs was strongly supported, and its subclass rank in the class Oligohymenophorea is reasonable; 2) the genus Epistylis might not be monophyletic, and the peristomial area, especially the peristomial lip, might be an important phylogenetic character within the genus Epistylis; 3) the taxonomic rank of the genus Carchesium and the genus Campanella were suggested to be adjusted; 4) Opisthonecta probably diverged from peritrichs with stalks; 5) the phylogenetic tree of peritrichs was reconstructed based on the molecular information inferred from SSrRNA gene sequences and the morphology. Moreover, the geographic distribution pattern of Carchesium polypinum in eight provinces of China that there were Northen and Southern population separated along the delineation between Yangtze River and Pearl River, maybe result from two factors: the vicariance resulted from the formation of the delineation between Pearl River and Yangtze River accompanying with the uplift of Qinghai-Xizang Plateau, and the different dispersal paths of C. polypinum affected by climate.