Crop domestication events followed by targeted breeding practices across plant taxa was a pivotal achievement for human civilization to introduce superior agronomic traits needed to meet human needs, and adapt varieties to local agronomic environments. However, domestication also caused a strong reduction in the genetic diversity of modern cultivars compared to their wild relatives. It remains undetermined how plant domestication may have influenced plant interaction with aboveground pathogens and belowground beneficial microbes. We examined the levels of induced resistance and changes in hormonal signaling pathways by Trichoderma harzianum, a beneficial soil microbe, against two foliar pathogens (Botrytis cinerea and Phytophthora infestans) in 30 diverse tomato genotypes across a domestication gradient, including wild relatives, landraces and modern commercial cultivars (conventionally or organically bred). Our results have demonstrated that Trichoderma enhanced both aboveground canopy and belowground root biomass in all tested genotypes. Wild relatives and landraces tomato were more responsive to Trichoderma against foliar pathogens in comparison to early modern cultivars. In addition to these finding, transcriptional profiling of responsive and non-responsive genotypes will be discussed. These findings have important implications for understanding the mechanisms behind differences in the induction of resistance among genotypes, and may someday be used to identify molecular markers for efficient selection of responsive cultivars.