Background: The purpose of this study is to describe the morphological characteristics of the Aphanizomenon spp. and related species from the natural samples collected in the Nakdong River of South Korea. Aph. flos-aquae was similar to Aph. klebahnii, whereas these species differed from each other by the size and shape of fascicles, which was macroscopic in Aph. flos-aquae and microscopic in the Aph. klebahnii. One of their characteristics was that trichomes are easily disintegrating during microscopic examination. C. issatschenkoi could be clearly distinguished from other species by hair-shaped terminal cell. Its terminal cell was almost hyaline and markedly pointed. Young populations of the species without heterocytes run a risk of a misidentification. Aph. skujae was characterized by akinete. Morphological variability of akinetes from natural samples collected in the Nakdong River was rather smaller than those reported by previous study. Conclusions: C. issatschenkoi are described for the first time in the Nakdong River. In addition, Aph. klebahnii and Aph. skujae are new to South Korea.