Objective To investigate the genetic phenotypes of Pseudomonas aeruginosa isolates from naval divers, so as to obtain the epidemic character of Pseudomonas aeruginosa isolates in different naval divers. Methods A total of 64 Pseudomonas aeruginosa strains from naval divers were sequenced by multilocus sequence typing (MLST) using 7 house-keeping genes: acsA, aroE, guaA, mutL, nuoD, ppsA and trpE. The sequencing results were analyzed based on Pseudomonas aeruginosa international MLST database to obtain the allelic profiles and sequence types (STs). MLST data were analyzed by Bionumerics 4.0 (http://pubmlst.org/mlstanalyse) using LIAN, SplitsTree and eBURST. Results Data from MLST revealed a high diversity among the strains. Out of the 64 strains, 53 strains could be assigned to 19 STs and 11 could not be assigned. ST274 and ST260 were the dominant strains, with ST274 accounting for 18.75% (12/64) and ST260 accounting for 15.62% (10/64). Conclusion Pseudomonas aeruginosa strains in naval divers have high diversity and preponderant genotypes. MLST is of great significance for Pseudomonas aeruginosa genomic study and epidemiology surveillance.