Abstract The distribution of archaeal lipids, including archaeol and glycerol dibiphytanyl glycerol tetraethers (GDGTs), in dolomite concretions and surrounding sediment from the Monterey Formation (Miocene) and the Sisquoc Formation (Miocene–Pliocene) were examined to distinguish planktic from benthic contributions. For this purpose, dolomites with positive δ 13 C values (+7‰ to +13‰) were chosen; such highly positive values point to pronounced methanogenesis of benthic archaea in the sedimentary column. At first glance, distributions and relative abundances of GDGTs in both dolomites and background sediment were similar, resembling patterns of marine planktic crenarchaea. A contribution of benthic euryarchaea to the GDGT pool became evident only from variations in the δ 13 C values of different biphytanes obtained after ether cleavage of GDGTs. Whereas bi- and tricyclic biphytanes had an isotopic signal typical of planktic archaea (δ 13 C −23.6‰ to −20.5‰ and −23.4‰ to −21.2‰, respectively) for both dolomite and background sediment, acyclic and monocyclic biphytanes showed lower values for dolomite samples (−25.1‰ to −22.6‰ and −27.6‰ to −24.7‰, respectively), indicating a contribution of lipids from benthic archaea. The isoprenoid diether archaeol (δ 13 C −23.9‰ to −22.9‰), assigned to euryarchaea, was only detected in dolomite samples, also reflecting additional input from sedimentary archaea, probably autotrophic methanogens. The occurrence of lipids derived from methanogenic archaea agrees with the strong 13 C-enrichment of dolomites and with mineral formation taking place in the zone of archaeal methanogenesis. This implies that the lipid biomarker inventory of sedimentary strata needs to be interpreted carefully, as it is often not straightforward to discriminate between input from the water column and sedimentary microbial activity.