The genus Scenedesmus and other allied morphospecies can not only been identified morphologically due to their smaller sizes and phenotypic plasticity. In this study, six Scenedesmus-like species were isolated and investigated from the inland freshwater of Ergene River Basin (Thrace, Turkey). These strains were studied in-depth using the light microscopy (LM) and the molecular ITS1-ITS4 gene sequencing. The combined morphological and phylogenetic analysis revealed that the strains studied belonged to the genera Desmodesmus (2 strains were characterized as D. communis and one strain identified as D. armatus var. subalternas), Acutodesmus (2 strains related to A. obliquus), and only one strain of the genus Pectinodesmus that identified as P. pectinatus. This study confirms that morphological identification of Scenedesmus-like species is considered not only enough for accurate species delineation but also the molecular approaching techniques should be applied. However, more deep molecular studies using other genes sequencing should be integrated for more easily species identification.