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In present investigation, consortia of two indigenous heterocystous cyanobacteria, Nostoc ellipsosporum HH-205 and Nostoc punctiforme HH-206 isolated from a salt affected area of Hisar, Haryana (India) were used as biofertilizer in bioremediation of salt affected soils having high electrical conductivity (13.5 dS/m) and pH (8) with poor organic carbon (0.3%) as well as nitrogen content (0.008%). The experiments were conducted in a pot house for the period of 240 days. There was a significant (P < 0.05) increase in carbon, phosphate, nitrogen, potassium, magnesium, cation exchange capacity, mean weight diameter and hydraulic conductivity of soil with biofertilizer treatment whereas sodium ion and electrical conductivity were found to be decreased. Improvement in soil aggregation and stability due to increased soil microbial activities (dehydrogenase, invertase and phosphomonoesterase) were also observed. Significant increase in growth and yield of pearl millet-wheat crop was observed in amended pots even under low water regime. Thus, the indigenous cyanobacterial species show promise in effective exploitation for phytoremediation and improved productivity of saline soils under semi-arid condition.