The complete 18S rDNA and ITS-2 sequences of two strains of Scenedesmus arcuatus were determined and subjected to phylogenetic analyses. Furthermore, ITS-2 sequences of Scenedesmus obtusus, of S. hindakii, and of Acutodesmus regularis were investigated. Phylogenetic analyses indicated that S. hindakii is most closely related to S. raciborskii and/or S. obtusus, embedded in the Scenedesmuscluster. The morphologically similar S. arcuatus and its variety platydiscus branched outside the Scenedesmus/Acutodesmus cluster (18S) or together with A. regularis and A. pectinatus (ITS-2). Therefore, the genera Acutodesmus and/or Scenedesmus are paraphyletic. S. arcuatus is not closely related to S. hindakii.