This study aimed to investigate molecular taxonomic diversity of unicellular chlorophyte strains in the northern Anatolian freshwater habitats of Turkey. Five strains were isolated from various habitats i.e. salty lagoons, shallow lakes, or slow-flowing creeks. The habitats chosen were Cernek lagoon (Kizilirmak Delta, Samsun), Kara lake (Cubuk, Ankara), Sarikum lagoon (Sinop), and Sirakaraagaclar creek (Sinop). Although the observations based on light microscopy showed no significant differences in cell morphologies, phylogenetic analysis based on nucleotide sequences of nuclear 18S rDNA and chloroplast 16S rDNA regions suggested that our isolates are related to 3 chlorophyte species: Chlorella vulgaris Beijerinck (S705, S706, and S708), C. sorokiniana Shihira & Kraus (A102), and Heterochlorella luteoviridis (Chodat) J. Neustupa, Y. Nemcova, M. Elias & PSkaloud (S705). This study represents the first records of C. sorokiniana and H. luteoviridis species for the algal flora of Turkey.