Significant areas of temperate bogs have been damaged by peat harvesting. After abandonment and spontaneous regeneration, these secondary mires can become important methane sources towards the atmosphere (Basiliko et al., 2007). Recent studies have shown the importance of methane oxidising bacteria (MOB) for the recycling of carbon from methane effluxes (e.g., Dedysh et al., 2001; Raghoebarsing et al., 2005). We set up a factorial experiment that allowed us to tests the effects of three levels of naturally fluctuating water table depths (13, 22, 35 cm) crossed with the effects of four different litter types (control, E. vaginatum, E. angustifolium, S. fallax). With help of improved 16 rRNA fluorescent in-situ hybridisation techniques we quantified the number of type II methane oxidising bacteria (MOB) living at different depths and just bellow the surface. The results show that the water table can strongly influence the active type II methan-otrophs living in the first 5 cm of the regenerating bare peat. These methane oxidis-ing bacteria were also hampered by the presence of plant litter placed on top of the bare peat surface. This could have important implication for the methane oxidation potential of methane and on restoration management practices.