Phylum Ciliophora is monophyly, and there are more than 10,000 species of ciliates in the literatures so far. Even after many times of modification on the classification of phylum Ciliophora by the observations on morphology, morphogenesis and ultrastructure, there are still arguments on many taxa. In this study, we developed novel methods to collect and treat samples which have different living habits and environments, and studied on phylogeny of ciliates by analyzing the sequences of Small Subunit Ribosome RNA (SSU rRNA) genes. We sequenced the SSU rRNA genes of 9 ciliates in 6 genus in this study. Among these species, there is no literature on the study of sequence and molecular evolution for 7 of them. After analyzing the phylogenetic tree and comparing the results with the characteristic in morphology and taxonomy, we have following conclusions: 1) Because of the coevolution in trichodinids, there are obvious difference between order Mobilida and order Sessilida in phylogenetic tree. The peritrichs is probably not monophyly. Due to the similar effect from coevolution with hosts on Hemiophrys macrostoma, there are deviations in the phylogeny for Hemiophrys macrostoma and Hemiophrys procera. It was found that class Litostomatea which Hemiophrys is belong to is not in the same clade with class Prostomatea in the phylogenetic tree,which confirms the change to remove the class Prostomatea from the subphylum including these two classes. The two characteristics of Stentor, having pigment granules and symbiotic Chlorella is apomorphic character, but not plesiomorphic character. There is well-fit ordination in evolution in gene level and the behavior level for budding reproduction of Suctoria. The possible evolution path for budding reproduction is: exogenous budding → endogenous budding → evaginogenous budding. 6) There is no obvious difference between Oxytricha and Stylonychia in both sequence and morphology. So there is no enough evidence for establishing these two genera. In addition, we found that the results from the morphological taxonomy and molecular phylogeny study fit each other, though there are some exceptions. The exceptions might be caused by the possibility that the same name is given to actually different species. So we suggest that morphology and molecular characters to a type specie should be submitted in the report for further taxonomic and phylogenetic research.