In a context of climate change peatlands may switch from a sink to a source of carbon (C). The induced positive feedbacks are closely linked to C dynamics, and thus to the fate of organic matter (OM) in the underlying peat. Our aims were to determine how moisture conditions in a Sphagnum-dominated peatland affect the dynamics of diagenetic sensitive OM which is thought to be the most reactive to warming effects. The approach was based on the identification of combined bulk and molecular bioindicators of OM sources and decay of peat profiles (up to 50 cm in depth) from two moisture conditions of the Le Forbonnet peatland (Jura Mountains, France). The (xylose+arabinose)/(galactose+rhamnose+mannose) ratio derived from the analysis of neutral monosaccharides was used to obtain indications on the botanical origin of the peat and tended to indicate a greater contribution of Cyperaceae in the deepest parts of the peat. Most bioindicators showed that OM decay increased with depth and was higher in the driest conditions. In these conditions, decay was shown by a loss of diagenetic sensitive oxygen-rich OM, probably leached by water table fluctuations. Decay intensity was also shown by the high ribose and lyxose contents at the peat surface, where microscopic observations also revealed relatively large quantities of fungal hyphae. The sugars could have arisen from microbial synthesis, primarily protozoan and fungal activity. These results suggest that water level changes preferentially impact biochemical changes in diagenetic sensitive OM, believed to be sensitive to drought events.