Karyotype structures ofScenedesmus acuminatus (Lagerch.) Chod. andScenedesmus pectinatus Meyen are compared. The karyotype ofS. acuminatus (n = 5) is described for the first time. It reveals four large metacentric and one large submetacentric chromosomes (4M + 1SM). The established karyotype differences have been helpful in clarifying the taxonomic position of these two species. The cytological analyses of other related clonal cultures suggest an evolutionary transition fromS. pectinatus towardsS. regularis throughS. pectinatus f.regularis, which correlates with the morphological data about their variability. These results are discussed from the cytogenetic, morphological and evolutionary point of view. On the basis of the karyotypic analysis, it was confirmed that from a taxonomic point of viewS. pectinatus, S. acuminatus andS. regularis are separate biological species.