Mycorrhizal fungi species Glomus fasciculatum was used to determine its effects on tomato growth, yield, fruit properties, nutrient uptake and substrate ion accumulation of plants grown hydroponically under open and re-cycling (closed) perlite substrate. AM inoculation in both open and closed soilless systems did not increasingly influence the vegetative plant growing and nutrient uptake of tomato cultivar M19. However, fruit yield absolutely increased with inoculation. AM inoculated tomato plants could effectively use photo assimilates for fruit production instead of vegetative growing. In the closed system with AM, ion accumulation and EC increases (salinity effects) were well controlled. Results indicated that mycorrhizal inoculation improved yield and fruit size, which can help alleviate deleterious effects of re-cycling soilless systems for tomato crop.