The extractable ester‐linked and the lipopolysaccharide (LPS) normal and hydroxy fatty acids of the methylotrophic bacteria Methylosinus trichosporium 0B3B, Methylobacterium organophilum XX, grown on methane and methanol, Mb. organophilum RG and Methylomonas sp. were analysed by capillary gas chromotography‐mass spectrometry (GC‐MS). Precise monounsaturated double bond position and geometry was determined by GC‐MS analysis of the derivatized fatty acids. The three species were readily distinguished based on the extractable fatty acid and LPS hydroxy acid profiles. Type I and Type II methylotrophs can be separated based on the presence of 16‐carbon and 18‐carbon monoenoic fatty acids in the two groups of organisms, respectively. Relatively novel components, 18: 1ω8c, 18: 1ω8t, 18: 1ω7t and 18: 1ω6c were present in Ms. trichosporium, and 16: 1ω8c, 16: 1ω8t, 16: 1ω7t, 16: 1ω5c and 16: 1ω5t were detected in Methylomonas sp. These specific lipids may be used, together with other components, as signatures for these methylotrophic bacteria in manipulated laboratory and environmental samples.