Species in the green algal order Cladophorales inhabit a wide range of aquatic ecosystems and display significant morphological variation. Identifying these species can be challenging due to their simple morphologies, which offer few diagnostic features. Furthermore, several characters exhibit extensive intraspecific variation and overlap between species. As a result, DNA-based approaches have become essential for accurate species identification. Cladophora, the most diverse genus in the order, is widely distributed and functions as an ecological engineer by shaping aquatic habitats. Accurate species identification is therefore important for sustainable management and effective conservation strategies. This study combines morphological analysis with DNA-based methods, using partial nuclear large subunit ribosomal DNA (LSU rDNA) sequences, to identify Cladophora species collected from various regions of the Aegean Sea (Turkey), and some locations in Greece. Our findings confirm the presence of six Cladophora species (C. albida, C. hutchinsiae, C. laetevirens, C. prolifera, C. ruchingeri, and C. vagabunda), along with Cladophoropsis membranacea. While these species have been previously reported from Turkey, our study highlights the continued importance of DNA-based methods for accurate identification within the genus Cladophora.