The fluorescence emission and absorption spectra of single Anabaena sp. strain PCC7120 cells including vegetative cells and heterocysts have been studied in intact filaments in vivo with confocal microscopy and grating spectrography. The diameters of the excitation and detection areas in the cells are less than 1.0 μm. Heterogeneities within the same cell and among different cells are observed. The evident spectral heterogeneities in heterocysts, not reported previously, are attributed to the different stages of the evolution of phycobilisomes in heterocysts. The photosystem II in heterocysts were found to be not metabolized completely.