Decomposition of organic substances is one of the main processes responsible for the signatures of stable carbon and nitrogen isotopes (δ 13 C and δ 15 N) in soils and peats. However, the applicability of δ 13 C and δ 15 N signatures at the natural abundance level as indicators of the degree of peat decomposition is still debatable. We evaluated δ 13 C and δ 15 N depth patterns of peat cores sampled at nine sites in two nearby Alpine peat bogs with varying degree of organic matter degradation. Based on water table depths and past drainage intensities, the peat cores were divided into three degradation classes. We found similar overall depths patterns of δ 13 C and δ 15 N across the nine depth profiles and distinct differences between aerobic and anaerobic peat layers. Considerable differences in stable C and N isotope signatures of same depths were detected between profiles of the three classes, whereas depth profiles of peat cores with similar degree in peatland degradation were nearly identical. In the aerobic peat layers, δ 13 C and δ 15 N increased with depths at all study sites from 2.6‰ to 4.9‰ for δ 13 C and 3.2‰ to 7.0‰ for δ 15 N compared to the initial signatures of the plant biomass. Standardised δ 13 C of aerobic layers differ distinctly between slightly degraded peats at the open peat bog area, intermediately degraded peats at the tree-covered edge areas and strongly degraded peats at the former peat-cutting site. δ 13 C signatures of aerobic layers of strongly degraded peats were markedly more negative compared to the slightly degraded peats because of the selective 12 C losses by microbial respiration. δ 15 N were more positive at strongly degraded than at slightly degraded sites in both, aerobic and anaerobic peat layers. The uniform stable isotope ratios in the anaerobic layers deeper than the local maxima of the isotopic signatures support the assumption that minor 13 C fractionation occurs under anaerobic conditions. δ 13 C slightly declining with depth in the waterlogged layers of strongly degraded peat reflects the preferential utilisation and loss of labile organic compounds enriched in 13 C. δ 15 N of strongly degraded peats was higher compared to well-conserved peat. The close relationship between the measured δ 15 N to δ 15 N modelled based on C:N ratios and bulk densities supports the assumption that the δ 15 N signature is the result of isotopic fractionation by peat decomposition. We conclude that peat decomposition strongly affects the δ 13 C and δ 15 N depth profiles of peat bogs and most likely overrides other factors, such as differences between plant species, litter components, atmospheric δ 13 C shift during peat formation, temperature effects, or type of mycorrhizal symbiosis. © 2019 Elsevier B.V.