We assessed the impact of intercropping on the microbial communities in the rhizosphere of wheat (Triticum turgidum L. ssp durum) and pea (Pisum sativum L.). Using a RNA based approach coupled with bacterial phylum specific real time PCR, we found that the active bacterial communities in the wheat-pea association were distinct from those in the rhizosphere when crops were cultivated solely. This first explorative study showed that intercropping induced a synergetic interaction, which modified the structure of active microbial communities associated with roots by reducing the representation of Alpha-Proteobacteria and Acidobacteria while promoting Actinobacteria. The latter phylum harbors many species identified as growth promoting bacteria, calling for further analyses to better understand their function for intercropped cultures.