The order Trentepohliales is composed of a complex of five aerial genera of branched filamentous green algae, Trentepohlia, Printzina, Phycopeltis, Cephaleuros and Stomatochroon; polyphyly has been discovered in some of these genera and species. To clarify the diversity and some taxonomic problems in the Trentepohliales, we collected specimens from southern China and successfully cultured the majority of them. We carefully observed morphological traits and performed phylogenetic analyses based on new 18S and ITS rDNA sequences obtained during the present study. Our results suggested that the ostiole position of the zoosporangia might effectively indicate the main lineages of Trentepohliales, with reassessment of the genera Trentepohlia and Printzina required based on this ostiole positioning. However, further molecular investigation, particularly for the genus Phycopeltis, is required. Phenotypic plasticity was very common in Trentepohlia and Cephaleuros and the traditionally circumscribed taxa may not be reliable. In Cephaleuros, the lichenized species do not form a single clade and most species are paraphyletic. Additionally, we suggest that a lack of description of the internal systems could be one reason for the difficulties in species identification. Further taxonomic studies should focus on an emendation of Cephaleuros and elucidating the molecular diversity of Phycopeltis.