Two differently coloured strains of the genus Chroococcus were isolated from a cyanobacterial assemblage collected from the stony littoral of a backwater of the Danube River in southern Slovakia. When grown after isolation, both subcultures were similar morphologically and their growth parameters did not differ substantially, but their pigment content (PC: PE and carotenoid ratios), details in their morphology during their life cycles and slime production were different. Identical and different characters of both morphotypes remained stable during cultivation on both agarized and liquid media, even when the cultivation parameters were changed. Both of the subcultures were studied using electron microscopy and almost their complete 16S rRNA genes were sequenced, which showed that in terms of their genetic relationship there was a 96.4% sequence similarity and certain taxonomic interspecific differences between both subcultures were confirmed. The various chromatic modifications recorded in cyanobacteria and their ecological consequences are discussed. The results yielded further data on the changes that occur during the cyanobacterial differentiation processes and their genetic stabilization.