We have previously constructed the physical map of a cyanobacterium, Synechoystis sp. strain PCC6803 on the basis of restriction and linking clone analysis. Since a total of 82 genes and gene clusters have been isolated from this strain, most of which are involved in oxygenic photosynthesis, portions of their sequences were amplified by the PCR method and assigned on the physical map of the genome by hybridization with restriction fragments, ordered clones, which were obtained from cosmid and lambda libraries, and long PCR-products. An exception was the gene psbG2 which was mapped on an extra-chromosomal unit of 45 kb. Since genetic maps of some of genes assigned above, especially those for photosynthesis, have been reported for two other cyanobacterial strains, Anabaena sp. PCC7120 and Synechococcus sp. PCC7002, gene organizations were compared among the three strains. However, no significant correlation was observed, suggesting that rearrangement of genes occurred in the respective strains during or after establishment of the species.