Background The dspA (hik33) gene, coding for a putative sensory histidine kinase, is conserved in plastids (ycf26) and cyanobacteria. It has been linked with a number of different stress responses in cyanobacteria. Results We constructed an insertional mutant of dspA (ycf26) in Synechocystis 6803. We found little phenotypic effect during nitrogen starvation. However, when the mutation was combined with deletion of the pta gene coding for phosphotransacetylase, a more significant phenotype was observed. Under nitrogen starvation, the pta/dspA double mutant degrades its phycobilisomes less than the wild type and still has about half of its chlorophyll-protein complexes. Conclusion Our data indicates that acetyl-phosphate-dependent phosphorylation of response regulator(s) overlaps with DspA-dependent signalling of the degradation of chlorophyll-protein complexes (and to a lesser extent phycobilisomes) in Synechocystis 6803.