Cylindrospermopsis raciborskii and Raphidiopsis sp. are filamentous freshwater bloom forming cyanobacteria, which can co-exist in the same bloom, morphologically distinguishable because of the terminal heterocyst (N fixation cells) in C. raciborskii. C. raciborskii comprise strains which produce either Cylindrospermopsin (CYN) an hepatotoxin, Paralytic Shellfish Poisoning toxins (PSP toxins) or do not produce toxins. On the other hand, the few strains described from Raphidiopsis genus produce anatoxin-a (neurotoxin), CYN, or do not produce toxins. Regardless of these phenotypic differences, C. raciborskii and Raphidiopsis sp. are not differentiable at 16S rRNA sequence level (similarity higher than 99%). However, analysis of the 16S23S rRNA Internal Transcribed Spacer (ITS), from C. raciborskii strains (CYN-producing or non toxic) and one PSP toxin-producing strain morphologically classified as C. raciborskii strain D9 showed a 28bp deletion signature of Raphidiopsis strains in D9. Further analysis demonstrated that D9 was not able to fix nitrogen; supporting D9 classification within the Raphidiopsis genus. We sequenced the complete genome from C. raciborskii CS-505, a CYN-producing, and Raphidiopsis sp. D9, finding high similarity between both genomes. Although the genome size is different (3.9 and 3.3 Mbp), these strains share around 2500 genes with a percentage of similarity higher than 97% between them. The differences are restricted to mobility elements and genome repair. Is the nitrogen fixation a phenotypic character strong enough to classify these organisms in two different genuses? We propose that both species must be re-classified within one genus, Cylindrospermopsis.