In a search for efficient fungal endophytes that can promote crop production and/or increase crop tolerance to abiotic stress, we isolated and tested various species harbored by wild plants. Sixty-seven endophytic fungal isolates were obtained from drought stressed, poor soil habitats, and inland high salt areas. We extensively tested the roles of Ampelomyces sp. and Penicillium sp. isolates in improving tomato growth and yield. Under greenhouse and field trails, Ampelomyces sp. and Penicillium sp. endophytes proved effective in conferring positive benefits to tomatoes placed under stress as well as under normal growing conditions. Ampelomyces sp. conferred tolerance to tomatoes placed under drought stress in addition to enhancing overall plant growth and fruit yield in comparison to non-symbiotic plants under drought stress. Penicillium sp. conferred tolerance to tomatoes placed under 300 mM salinity stress in addition to enhancing root biomass in comparison to non-symbiotic plants. Both endophytes proved efficient in enhancing plant growth, stress tolerance, recovery, and fruit yield under optimal experimental conditions in comparison to non-symbiotic plants. Field testing of tomato yield showed increased yield of symbiotic tomatoes compared to non-symbiotic ones. This data suggests that both Ampelomyces sp. and Penicillium sp. share a promising potential for improving future agricultural production, particularly with the projected changes in climate in the future.