The aim of this study was to evaluate the identification accuracy and to acquire a preliminary analysis for antimicrobial resistance of Pseudomonas aeruginosa isolated from bottled water in 21 provinces of China in 2013.Methods PCR method based on eta2 and oprI genes was used in the rapid verification for Pseudomonas aeruginosa isolates, and biochemical method with Vitek GN cards was used as reference method. Broth microdilution method was used to obtain minimal inhibitory concentrations (MICs) of all 531 strains to 12 antibiotics belonging to 8 categories. Results eta2 and oprI genes were validated by target bands and eta2 was more specific. The results of biochemical test showed that the identification accuracy of all provinces was 100%. PCR method using two genes could achieve an accuracy over 95% with few false negative results. Among 531 Pseudomonas aeruginosa strains from 21 provinces in China, there were 62 (11.68%) drug resistanta isolates in all, and these strains showed the highest resistance to polymyxin B (5.27%), followed by aztreonam (4.14%) and meropenem (3.01%). 230 (43.31%) and 135 (25.42%) of the strains tested were intermediate to ticarcillin-clavulanate and ticarcillin respectively.Conclusion The accuracy of Pseudomonas aeruginosa identification in all provinces was qualified, and PCR test could be a rapid and accurate screening method for detecting Pseudomonas aeruginosa in combination with traditional biochemical methods. Compared with clinical isolates, Pseudomonas aeruginosa isolated from bottled water remained at low drug resistance level, but there was a potential tendency that strains may become more resistant to ticarcillin-clavulanate and ticarcillin to some degree, so regular monitoring was necessary to recognize antimicrobial resistance characteristics and tendency of Pseudomonas aeruginosa isolated from bottled water.