Abstract: The methods of GC/EIMS and GC/CIMS to the analysis of the permethylated derivatives of intact polar lipids from Natronobacterium magadii were developed.GC/MS has proven itself to be rapid and powerful method for the determination of these derivatives.EI mass spectrometry,as a hard ionization technique,produces a lot of low mass fragment ions,which provided much information for the elucidation of alkyl chains of dialkylglycerol ethers,while CI mass spectrometry produced singly charged protonated molecules and high mass fragment ions in elucidation of whole structures of the derivatives.