The aim of study was to investigate the effect of two mycorrhizal fungus species Claroideoglomus etunicatum and Rhizophagus intraradices on the uptake of macronutrients and on the growth and yield of tomato hybrid plants cultivated in an ecological system. The experiment was carried out at an ecological farm in Grądy in the Lublin province of Poland, for three years (2015-2017). The experimental treatments included plants inoculated with Claroideoglomus etunicatum, Rhizophagus intraradices and plants without mycorrhizal inoculation used as a control. The mycorrhization of tomato roots with Claroideoglomus etunicatum and Rhizophagus intraradices resulted in an improved uptake of Ca and K through the plants. The length of the tomato roots, especially for the cultivars treated with Claroideoglomus etunicatum, were statistically longer than those of the control. Tomato roots inoculation with both of the studied mycorrhizal fungus strains significantly influenced the number of tomato leaves and improved the health status of the plant. The yield of tomato was not significantly affected by mycorrhization but Claroideoglomus etunicatum, to a greater extent than Rhizophagus intraradices reduced the yield of diseased fruit compared to the control. Among the studied mycorrhizal fungus species, better results were obtained with the application of Claroideoglomus etunicatum as compared with Rhizophagus intraradices for all examined features. Mycorrhizal inoculation contributed to the better growth of the plants, it improved their health and may be beneficially applied in the ecological production of tomatoes.