Cladophora has a global distribution and provides a habitat and food for numerous organisms. However, the taxonomy of Cladophora is confusing and poorly defined. In this study, 69 freshwater and brackish-water Cladophora samples from inland China were collected, and both morphological and phylogenetic analyses of these samples were performed. The concatenated molecular phylogenies based on ribosomal DNA sequences showed that these inland samples belonged to two groups: freshwater Cladophora and non-freshwater Cladophora. The phylogenetic results showed that there were eight clades in the freshwater group. The results of morphological observation showed characteristic similarities among the clades, and the samples in each clade exhibited different degrees of phenotypic plasticity. The prediction model for internal transcribed spacer 2 secondary structure showed that freshwater Cladophora contain one ring structure with three main helices (helices I-III), in which the helix III-2 region was most variable. The high phenotypic plasticity and lack of diagnostic characteristics of the freshwater Cladophora group made delineating species difficult and challenging. Further sampling from a broader range in combination with more efficient molecular markers are necessary to clarify the taxonomy of Cladophora in the future.