<p>Ongoing peatland degradation calls for an efficient method to indicate peatland hydrology and the success of restoration effort. In previous studies we found specific depth patterns of 13C and 15N depending on peatland hydrology (drained, rewetted or natural), but were unable to find an explanation of these patterns. As degradation is mostly connected to drainage we assumed an increase of microbial activity. This microbial activity should then be imprinted in stable isotope signatures (15N, 13C) due to differences in microorganism communities, their metabolic pathways and nutrient sources. We aimed to find a link between our investigated isotope depth patterns to microbial community composition. Therefore, we conducted a phospholipid fatty acid (PLFAs) analysis. As a marker for bacteria we used PLFAs i-C15:0 and a-C-15:0 as well as the C18:2,9c as a marker for fungi. We studied two nutrient poor peatlands in Northern Europe: Lakkasuo (Central Finland) and Deger&#246; Stormyr (Northern Sweden). At all locations cores were taken from adjacent drained (or rewetted) and natural sites. At Lakkasuo drained site, we found a high humification index (HI, after van Post), shown by less plant residuals and a high amount of matrix. For Deger&#246; Stormyr the picture looks different. Above the drained horizon (high HI) peat was light, with a smaller amount of matrix and lots of plant residuals (low HI), like it was also seen in the natural cores. At the drained (and rewetted) sites we found distinct peaks in microbial PLFA concentrations, which correlate to the stable isotope peaks ("turning point&#8221;) we found before. At the 15N turning point, in the center of the drained horizon, overall microbial-derived PLFA abundance is also the highest. Furthermore, the overall microbial-derived PLFA abundance is positively correlated with 15N values (r<sup>2</sup>=0.5). Fungi-derived PLFAs are negatively correlated (r<sup>2</sup>=0.4) to 13C. Fungi-derived PLFAs showed the highest amount at the uppermost part of the drained horizon and low amounts in the waterlogged conditions below the drained horizon, whereas 13C showed lowest values at the surface and high values below the drained horizon. Our results suggest, that fungi dominate microbial metabolism in the upper, aerobic peat horizon. Downwards the drained horizon conditions slowly switch to oxygen limitation. Thus, fungal-derived PLFAs decrease whereas bacterial-derived PLFAs are increasing. The highest diversity of microbial-derived PLFAs is indicated by the 15N turning point. Below this point, oxygen is increasingly limited and concentrations of all microbial-derived PLFAs are decreasing down to the 13C turning point and the onset of the permanently waterlogged, anaerobic horizon. Cores from rewetted peatlands show no depth trend of 15N values above the formerly drained horizon and a low amount of microbial-derived PLFAs. Hence, we conclude that stable isotope values reflect microbial metabolism processes, which differ between drained, rewetted and natural peatlands. Additionally, stable isotope patterns reflect a switch in the predominant communities from fungi to bacteria within a drained horizon. Summing up, the PLFA analysis approved that stable isotope measurements can serve as a cost and work efficient monitoring tool for peatland history as well as peatland restoration success.</p>