The analysis of genome sequences of cyanobacteria has had a large impact on photosynthesis, ecology and biotechnology research.50 The present re-sequencing project delivers the new and complete sequence of the Synechocystis sp. PCC 6803 ‘PCC-M’, a substrain used in many laboratories and in several aspects close to the original isolate. Altogether, there are now chromosomal sequences for seven substrains of Synechocystis sp. PCC 6803 available: ‘PCC-M’ (this study); ‘PCC-P’ (positive phototaxis) and ‘PCC-N’ (negative phototaxis), both based on single colonies isolated from the PCC strain and designated according to their direction of phototactic movement;24 ‘GT-I’, the standard strain in Dr Ikeuchi's group;8 ‘YF’17 and ‘GT-S’,10 a current derivative of the original stock of Synechocystis sp. PCC 6803 from which the chromosomal reference sequence for ‘GT-Kazusa’ was determined in 19962 and for the large plasmids in 2003,20 whereas the three small plasmids had been sequenced already before.37,51,52