Objective: Provide data support for the source tracing and pollution prevention of Pseudomonas aeruginosa in drinking water in Hunan Province. Methods: According to the national food safety standards of GB 8538—2016, the bottled water was tested randomly collected from partial cities and counties in Hunan Province, and the whole genome sequencing and molecular traceability of the 18 strains of Pseudomonas aeruginosa were detected. The carrying of virulence genes and drug resistance genes was detected. Results: It was confirmed that four strains of Pseudomonas aeruginosa showed consistency in terms of geographical distance, genetic distance, pathogenic and drug-resistant genotypes, and it was presumed that there was the same source. Conclusion: The traceability analysis of Pseudomonas aeruginosa in drinking water and the analysis of virulence and drug resistance genes in drinking water can be realized by whole gene sequencing based on 16S rRNA and single-copy orthologous genes.