The simultaneous measurement of specific phospholipid ester-linked fatty acids (PLFA) and diether lipids was achieved using high temperature capillary gas chromatography (GC). A GC method was developed and used to simultaneously determine diether lipid and PLFA content in the same GC run. The key features of the method were a slow (10°C/min) temperature ramp through the fatty acid region of the chromatogram followed by a high temperature ramp where the diether lipid eluted. Using this method on both pure bacterial cultures and aquatic sediments, resolution was achieved of the diether lipid and the PLFA, including novel C16 and C18 monounsaturated fatty acids derived from methanotrophs.