[Objective] To study the effect of p-nitrophenol (PNP) on persisters of Escherichia coli and Pseudomonas aeruginosa and to analyze the transcriptome to illustrate the impact of PNP on persister formation.[Methods] Ofloxacin was used to determine the bacteria persisters number. Cell self-digestion assay was done and the effect of respiratory inhibitors carbonyl cyanide chlorobenzene hydrazone (CCCP) on bacteria persisters was studied as well. Based on analysis of bacterial transcriptome, two genes (cyoA and appC) associated with the formation of persistence were screened. Their expressions were confirmed by Real-time Fluorescence Quantitative Polymerase Chain Reaction (PCR). The association between the two genes and the formation of persistence was also checked by antisense oligodeoxynucleotide assay.[Results] PNP inhibited the respiration of E. coli and P. aeruginosa, thus increased the proportion of bacterial persisters. PNP concentration, PNP function time and the bacterial growth period affected the proportion of bacteria persisters. PNP and CCCP inhibited the self-digestion of E. coli and P. aeruginosa, including the changes in dissolved oxygen, protein degradation and cell size, and the integrity of RNA. The results from transcriptome analysis and Real-time fluorescent quantitative PCR showed that PNP addition decreased the expression of cyoA and appC in E. coli and P. aeruginosa. Through the antisense oligodeoxynucleotide inhibitory expression of cyoA and appC was found that bacteria persister proportion increased compared with the original strain.[Conclusion] PNP can increase the proportion of bacteria persisters by inhibiting the cellular respiration.