The nucleotide sequence of the genome of the cyanobacterium Synechocystis sp. PCC 6803 was determined by Kazusa DNA Research Institute in 1996 as the first genome of photosynthetic organism.1 After that, this strain has been serving as a standard of cyanobacteria in various areas of research, such as photosynthesis, stress response and metabolism.2 However, the sequenced strain (called Kazusa strain in the present study) is different from the stock in Pasteur Culture Collection (called PCC strain in the present study). In fact, the Kazusa strain is a derivative of a ‘glucose-tolerant’ strain, which was obtained by J.G.K. Williams in DuPont Institute.3 The published sequence of the Kasuza strain included some genes inactivated by a putative point mutation, a putative frame shift, or an Insertion Sequence (IS) insertion, such as a one in the pilC gene. The mutation within the coding sequence of the pilC gene was pointed out to be a possible reason for the non-motility of the Kazusa strain.4 A 154 bp deletion was also found in the GT strain with respect to the PCC strain.5 The location of some IS elements in the Kazusa strain is known to be different with respect to other GT and PCC strains.6 Even within the PCC strains, different strains having different light responses have been isolated.2 All these slightly different strains bear the common strain name PCC 6803, but we need to recognize differences in exact strains used in various studies. For this purpose, we will have to pinpoint the differences in genome sequences of various different strains.