We examined the effects of long-term (51 years) drainage on peat microbial communities using phospholipid fatty acid (PLFA) analysis. We analysed the peat profiles of natural and adjacent drained fen and bog sites. Viable microbes (i.e. microbial PLFA) were present in relatively large amounts even in the deepest peat layers of both peatland sites, a finding that warrants further investigation. Microbial biomass was generally higher in the fen than in the bog. Microbial community structure (indexed from PLFA) differed between the fen and bog sites and among depths. Although we did not exclude other factors, the effect of drainage on the total microbial biomass and community structure was not limited to the surface layers, but extended to the deepest layers of the fen and bog. Long-term drainage increased the total microbial PLFA biomass in the surface, subsurface and bottom layers of the fen, but decreased it in the surface and bottom layers of the bog site. Drainage also increased the characteristic FAs of Gram-positive and Gram-negative bacteria in the surface and subsurface layers of the fen, and decreased them in the bottom layers of the bog site. The characteristic fungal FA was only reduced in the surface layers of the bog site by drainage. Thus, by affecting the microbial community beyond the surface layers, long-term peatland water-level draw-down can alter the microbial contribution to deeper peat organic matter stabilization. This suggests that long-term drainage may have a more significant climate change effect than revealed by the surface layer analyses alone.