Attached or floating macroscopic cyanobacteria can be found in shallow waters and can be easily hand-collected, but their identification is often challenging due to their high morphological variability. In addition, many members of environmental samples lose their morphological adaptations under controlled conditions, making the integration of analyses of field populations and derived isolated cultures necessary in order to evaluate phenotypic plasticity for identification purposes. Therefore, in this study, twenty-nine macroscopic field samples were analyzed by Illumina sequencing and parallel optical microscopy. Some colonies showed the typical morphological characteristics of Rivularia biasolettiana, and others showed those of Rivularia haematites. However, other Rivularia-like colonies showed ambiguous morphologies, and some of them showed the phenotypic features of the new genus Cyanomargarita, which is virtually indistinguishable from Rivularia in the field. In all of the colonies, phylotype composition was highly heterogeneous, with abundances varying depending on the analyzed sample. Some colonies were dominated (97-99%) by a single phylotype, while in others, the percentage of the dominant phylotype decreased to approximately 50-60%. Surprisingly, the same dominant phylotype was found in R. biasolettiana and R. haematites colonies. The relationships between environmental and/or biological factors and morphological variability in these colonies are discussed.