A tropical planktic filamentous cyanobacterium, tentatively identified as Lyngbya robusta, recently increased in abundance in Lake Atitlan, Guatemala, and since 2008 annual water-blooms occurred. This was one from the first known cases of L. robusta water-blooms worldwide. A polyphasic evaluation of L. robusta using 16S rRNA gene sequencing, cytomorphological markers, and ecological characteristics was made. This species had several unique features. It produced aerotopes that were irregularly spaced in cells; cyanotoxins were not found, and it fixed nitrogen in spite of the lack of heterocytes. It contained a high amount of carotenoids, which caused an unusual brown color of the macroscopic scum on the water level. Molecular phylogenetic analyses using the 16S rRNA gene showed that L. robusta, together with few other planktic species, formed a clade, separated from typical Lyngbya species. The main diacritical markers of this clade were the planktic type of life and formation of gas vesicles in cells. Based upon molecular, morphological and ecological data, a new genus Limnoraphis was proposed with four species.