DNA-SIP technology was used to detect active BaP-degraders involved in the biodegradation of benzo [a] pyrene (BaP) in two soils separately and in mixture. The lowest BaP removal was observed in red soil, and Ramlibacter (OTU830) belonging to the γ-Proteobacteria was labeled as BaP degrader with ¹³C-BaP. The highest diversity of degrading microorganisms occurred in the paddy soil with OTUs belonging to Nocardioids, Micromonospora, Saccharothrix, Lysobacter and Methylium present and a BaP removal efficiency of 29.5% after 14 d. BaP degraders in the mixed microbiome of the soil mixture were Burkholderia and Phenylobacterium, together with Nocardioides and Micromonospora as in the paddy soil. These results indicated that the active BaP-degraders in the mixed microbiome were identical to the active BaP-degraders in paddy soil (OTU356 and OTU328), but also unique in the mixed microbiome, such as OTU393 and OTU392. The functional genes of PAH-ring hydroxylating dioxygenases (PAH-RHD_α) were expressed and were positively related to the removal of BaP, and the active BaP degrading bacteria included both Gram-positive and Gram-negative bacteria. Saccharothrix, Phylobacterium, Micromonospora and Nocardioids are here reported as BaP degraders for the first time using DNA-SIP.