The FLIM (fluorescence lifetime imaging microscopy) technique allows picosecond fluorescence measurements at the level of the individual cell. Using this technique we were able to observe heterogeneity of cyanobacterial cells in a culture grown under controlled conditions and we were able to resolve structural variations within individual cells. It can be concluded that on the one hand the inhomogeneous distribution of photosynthetic pigments within the cell leads to variation of the fluorescence intensity, whereas on the other hand it is impossible to detect variation in the relative amounts of photosystem I and II throughout the cell. Different Synechocystis sp. PCC 6803 strain lines were compared to each other and differences were observed in the average fluorescence lifetimes obtained for individual cells of the various cell lines. The differences can be traced back to variable efficiency of excitation energy transfer from the phycobilisome antenna to the photosystems. We could successfully demonstrate that there is heterogeneity inside individual cells, within individual cultures, and between various wild-type cell lines.