The effects of metal ions on the biodegradation of benzene and toluene were investigated. Among 12 tested metal ions, Cu2+, Ni2+, Co2+ and Ag+ inhibited the degradation of benzene and toluene severely by Alcaligenes xylosoxidans Y234. Cu2+ was found to inhibit catechol 1,2-dioxygenase in the degradation of benzene and toluene. Co2+ and Ni2+ were supposed to inhibit benzoate 1,2-dioxygenase, while Ag+ was supposed to inhibit benzaldehyde dehydrogenase in the degradation of toluene. The inhibition effect caused by these metal ions could be overcome both by microbial adaptation and by adding specific aromatic compounds to the broth.