[Background] The suppurative disease, a bacterial infection caused by Pseudomonas aeruginosa and relatively difficult to prevent, has been a difficult problem in the domestication and breeding of forest musk deer. Currently, no vaccine is available. [Objective] To study the status of infection and molecular epidemiology of P. aeruginosa. [Methods] P. aeruginosa strains were isolated from two forest musk breeding centers in Zhenping County, Shaanxi Province and Baoxing County, Sichuan Province from October 2014 to October 2015, as well as their drug resistance was tested by traditional bacteriological methods. The fingerprint data bank of all strains was established by pulsed field gel electrophoresis (PFGE) typing, PFGE data were analyzed by BioNumerice software to reveal the prevalence pattern, and the pathogenicity of some isolates was analyzed. [Results] In total 60 P. aeruginosa strains were isolated, of which 34 were isolated from Zhenping, and 26 were isolated from Baoxing. The isolated P. aeruginosa strains were resistant to 17 antimicrobial agents at different levels, and the isolates from different area or different samples exhibited similar resistance phenotype. Multi-resistance was observed among the P. aeruginosa isolates, most of them exhibited multidrug-resistance to 5 and 6 antimicrobial agents. PFGE spectrum similarity of the 60 strains was between 49.1% and 100%, and A to O 15 PFGE types were obtained through cluster analysis, C, E, G, J were the dominant types. The virulence experiment on mice (LD50) suggested that the strains from animals were far more virulent than those isolated from the environmental, and the dominant bacterial type (E, F, J gene type) were more virulent than other strains. [Conclusion] There was horizontal transmission path with P. aeruginosa in different areas. The data provide a basis for prevention and treatment of suppurative inflammation in the captive musk deer.