RATIONALE Glycerol‐based alkyl ether lipids are ubiquitous components in marine sediments. In order to explore their structural diversity and biological sources, marine sediment samples from diverse environments were analyzed and the mass spectra of widely distributed, novel glycerol di‐ and tetraethers were examined systematically. METHODS Lipid extracts of twelve globally distributed marine subsurface sediments were analyzed by atmospheric pressure chemical ionization mass spectrometry (APCI‐MS). Tandem mass (MS/MS) spectra of compounds were obtained with a quadrupole time‐of‐flight (qTOF) mass spectrometer. RESULTS In addition to the well‐established isoprenoidal glycerol dialkyl glycerol tetraether (isoprenoidal GDGT) and branched GDGT, suites of novel lipids were detected in all studied samples. These lipids include the following classes of tentatively identified compounds: isoprenoidal glycerol dialkanol diether (isoprenoidal GDD), hydroxylated isoprenoidal GDGT (OH‐GDGT), hybrid isoprenoidal/branched GDGT (IB‐GDGT), hydroxylated isoprenoidal GDD (OH‐GDD), overly branched GDGT (OB‐GDGT), sparsely branched GDGT (SB‐GDGT) and an abundant H‐shaped GDGT with the M+H+ ion of m/z 1020 (H‐1020). CONCLUSIONS Characteristic MS/MS fragmentation patterns provided mass spectral 'fingerprints' for the recognition of diverse and prominent glycerol ether lipids. The ubiquitous distribution and substantial abundance of these glycerol ethers, as well as their structural variability, suggest a significant ecological role of their source organisms in various marine environments. Copyright © 2012 John Wiley & Sons, Ltd.