Citrus is grouped under the salt sensitive crops. Mycorrhizal fungi, a symbiotic relationship between plant roots and beneficial fungi, are supposed to impart the stress tolerance in the host plants. The stress tolerance improved due to Arbuscular Mycorrhizal fungi (AM fungi) colonization can be attributed to enhanced mineral nutrition. In the present study the efforts are made to evaluate the effectiveness of AM fungi with two citrus genotypes under salt stress. Three-month-old seedlings of Karna Khatta (Citrus Karna) and Troyer Citrange (Poncirus trifoliata × Citrus sinensis) were inoculated with the indigenous soil based AM inocula (mixed strains). The salinity gradient was developed by frequent irrigation with NaCl (0, 50, 100, 150 mM w/v). The results indicated that all the physical parameters were affected with increasing salinity. The proline accumulation increased while the chlorophyll, calcium and magnesium contents decreased significantly with increasing salinity. In general, the decreased AM colonization did not show any significant effects under salt stress.