Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats. However, the taxonomy of Cyanobacteria remains unstable because of an inadequate taxonomic classification system. Taxa within Cyanobacteria have historically been classified using morphological traits, which is inadequate to categorize the diversity within this phylum. The aim of this study was to propose a new taxonomic framework for

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... acteria using whole-genome-based taxonomic analysis including in silico Genome-to-Genome hybridization (GGH), Average Amino acid Identity (AAI), Average Nucleic acid Identity (ANI), phylogenetic reconstruction using a set of conserved marker genes (MLST), and 16S rRNA gene sequences. Applying these genomic signatures to a set of 100 cyanobacterial genomes allowed 86 species and 43 genera to be identified, among which 32 species and 19 genera were found to be novel. By exploring changes in the relative abundances of the analyzed genomes throughout diverse marine and freshwater ecosystems, we determined the ecological niches occupied by these taxa, adding another level to our proposed taxonomic scheme.