An investigation was carried out to study the native mycorrhizal fungi of saline wetland rice ecosystems of Aghanashini and Kagal regions of Uttara Kannada district. Among the two geographical locations, Aghanasini region recorded the highest Arbuscular Myocorrhizal (AM) fungal species diversity compared to Kagal in all diversity measure like Shannon-weaver index, Margalef’s index for species richness, Simpon’s dominance index. Three efficient isolates UASDAMFAG8, UASDAMFAG10 and UASDAMFAG28 (tentatively identified as Acaulospora melleae , Glomus macrocarpum and Glomus aggregatum, respectively using INVAM website http://invam caf.wuv.edu) based on Phosphorus uptake, total dry biomass produced and peroxidase activity in paddy at 6 dSm-1 and 8 dSm-1 were selected for the microcosms studies. The results indicated that AM fungal consortium comprising of Glomus macrocarpum + Acaulospora melleae + Glomus aggregatum significantly increased the plant growth parameters, mycorrhizal root colonization, total glomalin content, relative chlorophyll content, proline content, phosphorus uptake and soil enzyme activity over uninoculated control paddy at 6 dSm-1 and 8 dSm-1salinity levels) Further, AM fungal consortium significantly enhanced proline content in rice (13.47 μmol g-1 FW and 14.06 μmol g-1 FW at 6 dSm-1 and 8 dSm-1 salinity levels respectively). Among the single AM fungal inoculants, Glomus macrocarpum recorded increased plant growth parameters, root colonization, total glomalin content, relative chlorophyll, proline content, phosphorus uptake and soil enzyme activity. The interaction between AMF and salinity levels revealed that the AM fungal consortium is promising in mitigating salinity stress at 6 dS m-1and 8 dS m-1 conditions over uninoculated control in influencing the growth, mycorrhizal parameters, physiological parameters, biomass and phosphorus content of rice plants. Hence, these AMF isolates can be harnessed for alleviating salinity stress conditions in wetland rice plants.