An accurate physical map of the genome of a cyanobacterium, Synechocystis sp. strain PCC6803, was constructed on the basis of restriction and linking clone analysis. The genome contained 6 recognition sites for AscI, 25 sites for MluI, and 31 sites for SplI, and the entire genome size was estimated to be 3.6 Mb. Sixteen genes or gene clusters, including those involved in the photosynthetic systems, were localized on the physical map of the genome by hybridization. In the course of the above analysis, two extra chromosomal units with approximate sizes of 110 kb and 125 kb were identified.