Stable isotope analysis was used to determine the distribution of methanogenic pathways at permafrost collapse scar bogs to test the hypothesis that microbial respiration and methane production are stimulated by the input of organic matter associated with permafrost degradation and collapse. An alternative hypothesis is that recently assimilated carbon produced by the fen-like vegetation (Carex, Eriophorum) growing in open water moats formed by the collapsing edge of these features stimulates microbial respiration. We found that CO2 reduction was the dominant pathway for methanogenesis within the Sphagnum areas that dominate the surface cover of these features, but relatively more acetate fermentation occurred near collapse scar moats. Methane emission and net CO2 uptake were correlated. Both were elevated in collapse scar moats and then decreased along a transect from the moats toward the center Sphagnum-dominated areas. There also appeared to be a shift toward relatively more acetate fermentation in deeper samples associated with increasing cation (calcium and magnesium) concentrations. Our results indicate that organic inputs from permafrost degradation alone do not appear to stimulate acetate fermentation. Permafrost decomposition provides conditions along the collapsing edge that are conducive to colonization by fen-like vegetation that stimulates acetate fermentation and increases methane production and emission rates.