This chapter shall provide a brief definition and introduction to biomarkers, as well as an overview and limitations when biomarkers—also called molecular markers or fossils—are applied in paleopedological research. While not all biomarkers are appropriate and relevant, for instance, leaf wax-derived n-alkanes can help contribute to reconstruct chemotaxonomically vegetation history. Other examples are bacterial-derived glycerol-dialkyl-glycerol-tetraethers (GDGTs) as membrane lipids allowing temperature reconstructions and benzene polycarboxylic acids (BPCAs) representing pyrogenic biomarkers resulting from biomass burning and indicating fire temperature. These three abovementioned tools are also applied to loess-paleosol sequences, whereas, for example, (hemi-)cellulose-derived sugar biomarkers are primarily used in paleolimnological studies particularly for identifying terrestrial (allochthonous) versus aquatic (autochthonous) organic matter input. In geoarchaeological studies, additionally the analysis of steroid biomarkers such as sterols, stanols, stanones, and bile acids has emerged as attractive but at the same time admittedly quite work intensive and demanding tool allowing to quantify and distinguish between fecal input from herbivores, ruminants, omnivores, and humans. Apart from analytical challenges and exciting potential for further methodological developments, each biomarker tool also faces limiting issues. For instance, while leaching or postdepositional root contamination is negligible for n-alkanes, a quite limited taxonomic resolution as well as degradation should be considered. Last but not least, both the n-alkane and sugar biomarker analysis can be complemented by compound-specific isotope analysis (CSIA), namely, 2H and 18O analysis, respectively, in order to reconstruct paleohydrology/climate. One of the most recent methodological developments is the coupled 2H-18O biomarker approach, dubbed “paleohygrometry.”