Polycyclic aromatic hydrocarbons (PAHs) and heavy metals are generally present in mixtures in the e-waste dismantling areas, posing serious health risk to the local people. Bioremediation has been considered as a promising approach for PAHs and heavy metals removal. In this study, we applied flow cytometry to obtain a better understanding of membrane potential (MP), apoptosis and cell cycle of Stenotrophomonas maltophilia affected by combined pollutants of benzo[a]pyrene(BaP) and Cu(II). The results showed that BaP was the main factor damaging the cell membrane and influencing the MP. S. maltophilia could even protect against upsetting situation by encouraging early apoptosis, whereby compromised cells committed suicide, as a result, which, in turn, facilitated the metabolism of the bacteria with high-vitality. Furthermore, even if the bacterial cell division was blocked and stopped reproduction, a large number of key enzymes inside cells could still be used for degradation of BaP. The expression of protein related to the transport and metabolism of BaP, regulation of redox reactions and phosphorylation in bacterial cell during bioprocess were evident different. (C) 2016 Elsevier B.V. All rights reserved.