Photoacoustic spectra (PAS) were obtained for the cyanobacterium Synechococcus (Anacystis nidulans) cells embedded in isotropic and stretched polyvinyl alcohol films. The polarized radiation with the electric vector changing in 30° intervals with respect to given direction in a sample plane was used. Two cyanobacterium strains, one with very low biliprotein content, second with normal amount of biliproteins were investigated. The polarized absorption and fluorescence spectra were also measured. Conclusions were drawn about the thermal deactivation occurring in differently oriented pools of chromophores and about mutual orientation of their transition moments. Thermal deactivation in carotenoids (Cars) of both strains was different. The ratio of Car thermal deactivation to the thermal deactivation of chlorophyll (Chl) was higher in cyanobacteria with lower content of biliproteins than in the strain with normal amount of these complexes. Hence biliproteins can play the role in excitation energy transfer from Cars to Chls. For complex biological samples, polarized PAS can be a more sensitive method to investigate the directions of the absorption transition moments than the widely used polarized absorption spectra. and A. Planner ... [et al.].