Two high quality Cyanobacteria MAGs were recovered from a freshwater lake, Brazil. The MAGs were identified as Raphidiopsis (=Cylindrospermopsis) raciborskii. The new MAGs increased the pangenome size by 11 % improving the core/pangenome ratio. Pangenome-based phylogeny confirmed SouthAmerican (SA) strains’ closer relationship. The SA clade distinctness, with unique saxitoxin producing ability, was reinforced.