Morphological features are not sufficient for species characterization in microalgae. There are many possibilities for existing characters. Recently, molecular techniques have been used in many areas and this technique increasing the reliability of the work done. The general purpose of the study is to compare Cyanobacteria and Chlorophyta species under the culture conditions using classical classification and molecular identification. In order to achieve this aim, isolation of different clonal cultures of Cyanobacteria and Chlorophyta species from Apa Dam Lake and Beykavagi pond (Konya, Turkey) and Eber Lake (Afyon, Turkey) was performed. Morphological diversity of Cyanobacteria and Chlorophyta species was observed under culture conditions and visualized by both light microscopy and scanning electron microscopy (SEM). In addition, phylogenetic relationships of these strains to 16S rRNA and 18S rRNA gene sequences were determined. According to DNA sequence analysis, 3 isolates were found to be similar to Chodatodesmus mucronulatus (Chodat) Bock & Krienitz (97%), Desmodesmus sp. (Chodat) T.Friedl & Hegewald (98%) and Pediastrum duplex Meyen (97%). Other 4 isolates were found to be similar to Fischerella ambigua (Kutzing ex Bornet & Flahault) Gomont (99%), Leptolyngbya sp. Anagnostidis & Komarek (97%), Phormidium autumnale Gomont (99%) and Rivularia sp. C. Agardh ex Bornet & Flahault (99%).