Molecular-genetic techniques provide a powerful approach to study photosynthetic and respiratory electron transport pathways in thylakoids of the transformable cyanobacterium Synechocystis sp. PCC 6803. Either or both of the photosystems can be genetically deleted from this organism, and resulting mutants can be propagated in the presence of glucose. This provides the opportunity for targeted mutagenesis of particular components of one of the photosystems, and analysis of resulting mutants has yielded useful information regarding residues or domains of protein subunits. In addition, by selection for secondary mutations neutralizing the functional impairment caused by an introduced mutation, the sequence flexibility and structural vicinity of domains can be determined. As an example, a preliminary characterization of a photoautotrophic pseudorevertant of the site-directed D2 mutant E69Q, which is an obligate photoheterotroph, will be presented here. Mutant analysis also has proven to be useful in the determination of the functional link between photosynthetic and respiratory electron transfer in cyanobacterial thylakoids. In Photosystem-I-less mutants, light-induced electron transport occurs involving water oxidation (oxygen production) in Photosystem II, and oxygen reduction by a terminal oxidase, thus without net oxygen production or consumption. The net result of this electron transport 'cycle' should be the generation of a proton gradient over the thylakoid membrane, which can be used for ATP production.