Abstract:[Objective] For establishing taxonomic relationships among Bartonella species, gas chromatography (GC) was utilized to investigate their cellular fatty acids (CFAs) compositions with particular attention on the different growth conditions in the qualitative and quantitative changes of CFAs. [Methods] The whole cellular fatty acid methyl esters (FAMEs), from the different base media and the media at different percent of sheep blood, subculture and temperature of incubation, were obtained by saponification, methylation or extraction and then analyzed using the Sherlock Microbial Identification System. The dendrograms of ten strains of Bartonella species, isolated from different hosts (cats, dogs, rats, voles and human), and nine Bartonella strains of cats from different areas, were generated based on the CFAs data matrix using SPSS 16.0 software package. [Results] There were 20 CFAs in Bartonella strains tested. Among them, seven CFAs were common components and detected in all tested type strains of Bartonella species, which include C18:1ω7c, C18:0 and C16:0 and account for more than 80% of the total CFAs. The rest were minor with their presence and relative contents of being affected significantly by differences of culture media and conditions. The dendrogram of the isolates from cats with different type strains was approximately consistent with the hierarchical structure of molecular phylogenetic systematics. [Conclusion] The CFAs profiles are obtained by carefully regulating and standardizing the growth conditions and these profiles are successfully used to identify B. henselae wild isolates. Although these CFAs profiles are very useful in terms of Bartonella taxonomy, they must be viewed with caution until our knowledge of the quantitative and qualitative distributions of fatty acids over a wide variety of taxa and the growth conditions.