The biphenyl/polychlorinated biphenyl degrading strain R04 (Rhodococcus sp. R04) and several model microorganisms were used as the research objects. Cell division and morphological changes of biphenyl/polychlorinated biphenyl degrading strain R04 were analyzed by high performance liquid chromatography, fluorescence microscopy and scanning electron microscopy under the conditions of biphenyl and its metabolites culture. The results showed that the division of Rhodococcus sp. R04 and several model microbial cells were inhibited under biphenyl and its metabolites culture conditions, and some microbial cells morphology were affected. Compared with the precursor-biphenyl and its metabolite 2-hydroxy-6-keto-6-phenyl-2, 4-hexadienoic acid, 2,3-dihydroxybenzene has stronger inhibition and morphological change on G⁺, G^- bacteria or Rhodotorula cell division. The proportion of R.R04 cells and defective R.R04 cells forming incomplete septum was increased under the condition of 2,3-dihydroxybenzene culture. It caused that 96.4% of E. coli BL21 cells surface was dented, cytoplasmic content was lost and bacterial body volume was shrunk. It caused that 89.6% of Bacillus subtilis cells was shrunk significantly. The phenomenon that Staphylococcus aureus has almost no cells to form a complete septum was caused. The percentage of Rhodotorula cells that could germinate and reproduce was decreased from 64.2% to 19.3%, but there was no significant change in cell morphology. Biphenyl metabolite 2,3-dihydroxybiphenyl has strongly inhibitory effect on cell division and proliferation of Rhodococcus sp. R04 and other microorganisms than its precursor-biphenyl, and it is suggested that the toxic effect of environmental compounds metabolism should be considered when the interaction between environmental compounds and microorganisms.