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Decomposition of organic substances is one of the main processes responsible for the signatures of stable carbon and nitrogen isotopes (delta C-13 and delta N-15) in soils and peats. However, the applicability of delta C-13 and delta N-15 signatures at the natural abundance level as indicators of the degree of peat decomposition is still debatable. We evaluated delta C-13 and delta N-15 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 delta C-13 and delta N-15 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, delta C-13 and delta N-15 increased with depths at all study sites from 2.6 parts per thousand to 4.9 parts per thousand for delta C-13 and 3.2 parts per thousand to 7.0 parts per thousand for delta N-15 compared to the initial signatures of the plant biomass. Standardised delta C-13 of aerobic layers differ distinctly between slightly degraded pests at the open peat bog area, intermediately degraded peats at the tree-covered edge areas and strongly degraded pests at the former peat-cutting site. delta C-13 signatures of aerobic layers of strongly degraded pests were markedly more negative compared to the slightly degraded peats because of the selective C-12 losses by microbial respiration. delta N-15 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 C-13 fractionation occurs under anaerobic conditions. delta C-13 slightly declining with depth in the waterlogged layers of strongly degraded peat reflects the preferential utilisation and loss of labile organic compounds enriched in C-13. delta N-15 of strongly degraded pests was higher compared to well-conserved peat The close relationship between the measured delta N-15 to delta N-15 modelled based on C:N ratios and bulk densities supports the assumption that the delta N-15 signature is the result of isotopic fractionation by peat decomposition. We conclude that peat decomposition strongly affects the delta C-13 and delta N-15 depth profiles of peat bogs and most likely overrides other factors, such as differences between plant species, litter components, atmospheric delta C-13 shift during peat formation, temperature effects, or type of mycorrhizal symbiosis.