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Cyanobacteria represent promising organic inputs in rice–wheat cropping system, as they contribute towards accretion of N and C, besides secreting growth-promoting substances which influence plant productivity and soil fertility. The present study focused towards using a combinatorial approach for evaluating field-level colonization of cyanobacteria in soil and their effect on soil microbiological and plant parameters, employing agronomic and molecular tools. A consortium of cyanobacterial strains (BF1, Anabaena sp., BF2, Nostoc sp., BF3, Nostoc sp. and BF4, Anabaena sp.) was employed in different three-and four-member combinations along with 75% N + Full dose of P and K fertilizers. A significant enhancement in microbial activity and plant growth/yields and savings of 25% N in the wheat–rice cropping sequence were recorded, especially in treatments involving 75% N + Full dose of PK+BF1+BF2+BF4 and …