81 Pseudomonas aeruginosa from Guangdong Provincial Institute of Food Inspection were identified by 16S rRNA sequence analysis. The DNA was isolated and the sequences of 16S rRNA gene were amplified by PCR with the bacterium universal primers, and then the PCR products were sequenced after 2% agarose gel electrophoresis. Moreover, the corrected sequences were aligned with Clustal X and the phylogenetic tree was constructed by MEGA5.1. Consequently, the identified results of the 81 strains confirmed their original identification before. On the phylogenetic tree, No. 24-3-QY strain formed a separate branch with No. 100-5-JM strain and No. 106-3-JM strain. No.2 8-1-DW formed one branch and the other 77 strains formed a separate branch with P. aeruginosa ATCC 27853. This was the first research about waterborne P. aeruginosa in Guangdong Province when China began to implement GB 19298—2014 “National food safety standards of packaged drinking water” since May 24, 2015. The waterborne P. aeruginosa culture collection in Guangdong was preliminarily established basing on these strains. These data will provide a powerful tool for effectively tracing source of P. aeruginosa and controlling the water contamination in future.