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Aims: Many studies have reported beneficial effects of yeasts on the colonization and development of arbuscular mycorrhizae, thought a few studies have also shown neutral effects. All these studies have in common that the mechanism, by which yeasts and mycorrhizae interact, is little understood. Here, we explore how plant growth-promoting yeasts affect the colonization of tomato plants by beneficial mycorrhizal fungi. Methods: We tested the influence of the soil yeasts Candida saitoana, Tausonia pullulans, and Saccharomyces eubayanus on colonization of tomato roots by the mycorrhizal fungus Rhizophagus irregularis. We analyzed mycorrhizal parameters and the expression pattern of mycorrhiza-specific genes. In plants co-inoculated with S. eubayanus and R. irregularis, we measured the root accumulation pattern of jasmonic acid, oxo-phytodienoic acid, abscisic acid and salicylic acid, and the expression of genes related to plant hormone signaling and metabolism. Results: The three yeasts had distinct effects on mycorrhizal colonization: C. saitoana had no effect on mycorrhizal parameters, T. pullulans delayed mycorrhizal colonization at an early stage, and S. eubayanus slowed colonization down throughout the entire trial. In plants co-inoculated with S. eubayanus and R. irregularis, we observed a sustained increase in jasmonic acid and up-regulation of the JA biosynthesis related genes LOXD, OPR3, and AOS1. Conclusion: Co-inoculation with yeast affected mycorrhizal colonization and altered the expression pattern of mycorrhizal and plant defense-related genes. In particular, the yeast S. eubayanus modified plant defense hormones such as jasmonic acid, which is linked to mycorrhizal-induced resistance in tomato plants.