Nucleoside diphosphate kinase (Ndk/NDK/NDPK) is known to possess pleiotropic functions, one of which is that as a protein kinase, and known to be involved in stress tolerance in plants. The role of Ndk in the ancient cyanobacteria, also known as the progenitor of chloroplast, has not been investigated. To assess the role in Nostoc PCC 7120, a recombinant strain overexpressing Ndk, Anndk+ was generated. Phosphoproteomic analysis of Anndk+ and its comparison with that of the vector control AnpAM revealed differential phosphorylation at S/T/Y sites of proteins belonging to varied functional groups, with the majority being from those involved in photosynthesis. A total of 177 phosphopeptides and 117 phosphoproteins were identified, some of which have been identified as a phosphopeptide for the first time in any cyanobacteria. Compared to AnpAM, the Anndk+ cells exhibited (i) lower photosynthetic efficiency and electron transport rate at low PAR (photosynthetically active radiation), (ii) no change in photochemical quenching across PAR, (iii) but distinct non-photochemical quenching [zero Y(NPQ) and high Y(NO) in Anndk+ and high Y(NPQ) and low (NO) in AnpAM], and (iv) increased tolerance to -radiation, oxidative, salt and DCMU stresses. The possible role of the change in phosphoproteome of Nostoc upon overexpression of Ndk in modulating photosynthetic parameters and abiotic stress tolerance has been discussed. This is the first report on a wide physiological role for nucleoside diphosphate kinase in any cyanobacteria.