Abstract: The rhizosphere microbiome, also referred to as the second genome of the plant, is crucial for plant health. Thus, it is the most important resource for biological control agents screening. Here we summarized the recent research development on relationship between plant and the rhizosphere microbiome: including how a plant shapes its rhizosphere microbiome actively; how the root microbiome act on the “rescue” mechanism; and how the biological control agents and the native microorganisms act on each other.