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Inoculation with plant growth promoting rhizobacteria (PGPR) might be a sustainable practice to increase nutrients use efficiency of crops. In order to elucidate the mechanisms underlying the beneficial interaction, an RNA-Seq transcriptional profiling of tomato leaves was performed after roots’ inoculation with <i>Azospirillum baldaniorum</i> (AB) or <i>Paraburkholderia graminis</i> (PG). Overall, 427 and 512 differentially expressed tomato genes were retrieved for AB and PB inoculation, respectively, and in both cases, the number of up-regulated genes exceeded the number of those down-regulated. Expression profiles suggest that the interactions between tomato seedlings and microorganisms are species-specific. The common activated pathways involved genes coding for proteins related to water and nutrients uptake, defense responses to biotic and abiotic stresses and hormonal regulation of fruit-set and ripening. While AB induced genes coding for MYB transcription factors known to be involved in response to biotic and abiotic stresses, PG upregulated 5 genes coding for putative late blight resistance protein homolog. Auxin responsive molecules and gibberellins involved in the fruit-set and early fruit growth in tomato were mainly induced by AB correlating to higher fruit number obtained in a previous field study. On the other hand, ERF transcription factors involved in ripening were induced mainly by PG treatment.