ObjectiveTo investigate whether gas chromatographic wholecell fatty acid analysis can be applied to analyze the homology of Pseudomonas aeruginosa. MethodsTwentysix multidrugresistant Pseudomonas aeruginosa（MDRPA） strains isolated from sputum samples of intensive care unit (ICU) patients were collected from January to December 2008. Pulsedfield gel electrophoresis (PFGE) and gas chromatographic wholecell fatty acid analysis were performed to analyze the homology. ResultsPFGE analysis revealed that 26 isolates had 6 clones; gas chromatographic wholecell fatty acid analysis showed that 26 strains had 4 clones, and consistent rate was only 26.92%（7/26）.ConclusionGas chromatographic wholecell fatty acid analysis is not identical with PFGE in analyzing homology of Pseudomonas aeruginosa.