Abstract We present an ecologically based biomarker method for estimating past salinity, especially in hypersaline conditions. The relative amounts of acyclic diether and tetraether membrane lipids synthesized by Archaea correlate with salinity from 0–250 practical salinity units (psu) in modern settings. We examined the preservation of this lipid biomarker–salinity relationship in ancient sedimentary organic matter using samples from two sequences of marls and diatomites deposited just prior to the Messinian Salinity Crisis. Salinity estimates were consistent with expected absolute salinity, as well as the amplitude of variations leading up to the Messinian Salinity Crisis. This lipid biomarker approach to salinity reconstruction complements existing paleosalinity proxies because (i) Archaea survive and thrive over a broad salinity range, well beyond that of haptophyte algae and other plankton which form the microfossil record and (ii) it provides fine salinity resolution for the wide range broadly defined as hypersaline. With the proxy, there is the potential to provide novel insights into salinity variation within desiccating basins in climatically sensitive seas (e.g. Dead Sea, Permian Delaware Basin), evolution of brines, timing of onset of hypersaline conditions and evaporite deposition.