Secondary structure analysis of 34 internal transcribed spacer 2 (ITS-2) sequences showed that the current model for the green algae Scenedesmus and Desmodesmus is not accurate. In particular, helix I of the currently used model showed considerable deviations from our new model. The newly proposed model is supported by many two-sided compensated base pair changes and fully compensated insertions in all four helices. Phylogenetic analysis by maximum parsimony based on the new alignment confirmed the recent division of the old genus Scenedesmus into the new genera Scenedesmus and Desmodesmus. However, the analysis was not able to show phylogenetic relationships within these two genera. Hence, the ITS-2 region alone is not suitable for clarifying the phylogeny of Scenedesmus and Desmodesmus and new regions have to be found for future sequence analyses.
