Abstract:In order to find a suitable molecular marker for the classification of Charophytes, some of the Charophytes were used as material to make a phylogenetic study by analyzing the diversity of 18S rDNA、rbcL、atpB and 18S rDNA、rbcL、atpB threegene combination and constructing the phylogenetic tree. The results showed that 18S rDNA gene was more suitable for the study of the classification between the genus and tribus, but further classification requires a more mutated sequences; though the rbcL and atpB sequences were more mutated than the 18S rDNA, they were not suitable for phylogenetic study of Characeae alone. There were some gaps in the interspecific and intraspecific genetic distance of the three gene combination analysis, and the interspecific genetic distance(0.002~0.097) was greater than intraspecific genetic distance(0~0.001). Meanwhile, the topological structure of the phylogenetic tree analyzed by three gene combination sequences was consistent with the traditional morphological classification structure, and the ambiguity of Chara classification was resolved in genus and tribus, the phylogenetic tree appeared a good topologic structure. In the summary, the 18S Rdna、rbcL、atpB threegene combination sequences analysis can separate some similar species of the Charophytes, and solve the classification problem of the Charophytes species selected in this study.