To demonstrate rhizospheric effect on the mechanism of (polycyclic aromatic hydrocarbon) PAH degradation, and to establish a proper joint phytomicrobial remediation mode, microcosms containing microorganisms and PAHs (pyrene and benzo $$a$$ Pyrene) were added with clover (Trifolium repens) root exudates to study their effects on PAH degradation. Dioxygenase gene and 16S rDNA gene copy number changes during the biodegradation process were analyzed, and the microorganism with a good ability for degrading PAHs was identified. The results showed that Mycobacterium M1 had the capability to degrade PAHs. When total organic carbon (TOC) concentration of clover root exudates was 35.5 mg·L^-1, pyrene and benzo $$a$$ pyrene degradation rates increased significantly, and the proportion of dioxygenase gene to 16S rDNA of Mycobacterium M1 increased. In the biodegradation process, dioxygenase gene copy number increased significantly, whereas 16S rDNA copy number increase was not so obvious, showing that the former was related to degradation process, but the latter was related to microbial numbers. It was concluded that the clover root exudates promoted the dioxygenase gene copy number of Mycobacterium M1, which contributed to the degradation of PAHs.