Abstract: The sequences of ITSregions and 5.8S coding region of nuclear ribosomal DNAfrom 16 species of the genus Chlamydomonas were determined and analysed.Based on the ITSsequences, the phylogentic tree of these species was constructed using the nrDNA ITSsequence of Ulothrix zonata as the outgroup.And on the basis of 12 morphological characters for study in the 16 species, phylogenetic analysis was performed and then Wagner method was used to construct the phylogenetic tree.Finally the two phylogenetic trees were compared and the phylogenetic affinity between the 16 species of the genus Chlamydomonas was analysed.The close affinity between tree pairs of species: C.incerta with C.reinhardtii;C.geitleri with C.noctigarna;C.asymmetrica with C.mexicana is supported by both nrDNA ITSanalysis and the morphological characters analysis.However, the result shows that there is significant difference between the phylogenetic tree from the nrDNA ITSsequences analysis and the phylogenetic tree from morphological characters analysis.The two phylogenetic trees don't agree with each other as a whole, and the possible reason for the difference is discussed.