The study and revision of the unicellular cyanobacterial genus Synechocystis was based on the type species S. aquatilis Sauv. and strain PCC 6803, a reference strain for this species. Uniformity in rRNA gene sequence, morphology, and ultrastructure was observed in all available Synechocystis strains, with the exception of the strain PCC 6308, which has been considered by some to be a model strain for Synechocystis. This strain differs substantially from the typical Synechocystis cluster according to both molecular (<90% of similarity, differences in 16S–23S rRNA internal transcribed spacer [ITS] secondary structure) and phenotypic criteria (different ultrastructure of cells). This strain is herein classified into the new genus Geminocystis gen. nov., as a sister taxon to the genus Cyanobacterium. Geminocystis differs from Cyanobacterium by genetic position (<94.4% of similarity) and more importantly by its different type of cell division. Because strain PCC 6308 was designated as a reference strain of the Synechocystis cluster 1 in Bergey’s Manual, the members of this genetic cluster have to be revised and reclassified into Geminocystis gen. nov. Only the members of the Synechocystis cluster 2 allied with PCC 6803 correspond both genetically and phenotypically to the type species of the genus Synechocystis (S. aquatilis).