Marine microorganisms adapt to their habitat by structural modification of their membrane lipids. This concept is the basis of numerous molecular proxies used for paleoenvironmental reconstruction. Archaeal tetraether lipids from ubiquitous marine planktonic archaea are particularly abundant, well preserved in the sedimentary record and used in several molecular proxies. We here introduce the direct, extraction-free analysis of these compounds in intact sediment core sections using laser desorption ionization (LDI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). LDI FTICR-MS can detect the target lipids in single submillimeter-sized spots on sediment sections, equivalent to a sample mass in the nanogram range, and could thus pave the way for biomarker-based reconstruction of past environments and ecosystems at subannual to decadal resolution. We demonstrate that ratios of selected archaeal tetraethers acquired by LDI FTICR-MS are highly correlated with values obtained by conventional liquid chromatography/MS protocols. The ratio of the major archaeal lipids, caldarchaeol and crenarchaeol, analyzed in a 6.2-cm intact section of Mediterranean sapropel S1 at 250-μm resolution (∼4-y temporal resolution), provides an unprecedented view of the fine-scale patchiness of sedimentary biomarker distributions and the processes involved in proxy signal formation. Temporal variations of this lipid ratio indicate a strong influence of the ∼200-y de Vries solar cycle on reconstructed sea surface temperatures with possible amplitudes of several degrees, and suggest signal amplification by a complex interplay of ecological and environmental factors. Laser-based biomarker analysis of geological samples has the potential to revolutionize molecular stratigraphic studies of paleoenvironments. molecular stratigraphy | solar cycle | laser desorption ionization | FTICR-MS | archaeal tetraether lipids M icrobial lipids in aquatic sediments reflect phylogeny, environmental conditions, and biogeochemistry of the water column in which they were produced. After sedimentation and because of the persistence of lipid structures in the sedimentary record, the information archived in these lipids remains available on geological time scales. Retrieval of this information from sediments and rocks has increasingly contributed to our understanding of past environments, microbial communities, and biogeochemical processes (e.g., refs. 1-5). Merged with the concept of molecular stratigraphy (2, 6), i.e., the analysis of selected biomarkers in solvent extracts of sediment samples in a stratigraphic framework, unique information can be gleaned regarding the temporal changes of past ecological and environmental conditions in aquatic systems. Because of analytical requirements, the temporal resolution is typically limited by centimeter-scale-sized samples, which, dependent on the depositional setting, tend to integrate time periods of decades to millennia, even in high-sedimentation settings such as the Santa Barbara Basin...