The genus Synechocystis represents a polyphyletic taxon of cyanobacteria. The analysis of 16S rRNA gene sequences of 30 strains from the СALU collection (http:// researchpark.spbu.ru/collection-ccem-rus/1628-ccem-kollekciya-calu-rus) previously identified as Synechocystis spp. empowered to distinguish three phylogenetic clusters at generic level: «сluster Synechocystis sensu stricto» (21 strains), «cluster geminocystis» (5 strains), and «cluster biofilms» (4 strains). According combined phenotypic and genotypic characters, «cluster biofilms» (strains CALU 1077, 1127, 1173, and 1174) can be described as a new genus of unicellular cyanobacteria containing three species. The strains of «cluster geminocystis» (CALU 1334, 1759, 1794, 1801, 1807) represent a new species within the Geminocystis genus.