Sphagnum mosses are adapted to thrive in cool, nutrient-poor acidic environments. Nitrogen (N2)-fixing and methane (CH4)-oxidising microorganisms living as epiphytes and endophytes on and in Sphagnum mosses are known to support Sphagnum growth. We explored how these processes combined with the microbial community link to different Sphagnum moss species, sites and moss segments (capitulum or shoot), using Sphagnum palustre and Sphagnum fallax sampled from two field sites and separated into upper (capitulum; 0–3 cm) and lower (shoot; 3–6 cm) segments. The results of 16S rRNA gene amplicon sequencing showed that the microbial community composition is both site- and moss-specific. The microbial activity, measured as 15N-N2 fixation (6.5  0.9 µmol g-1 d-1) and 13C-CH4 oxidation (0.5  0.1 µmol g-1 d-1), differed between field sites but not between moss species. The CH4 oxidation was higher in the upper moss segments. On the basis of these results we hypothesise that the discrepancy between microbial activity and microbial community composition at moss-species level may be caused by functional redundancy; although microbial communities vary between Sphagnum species, they can function similarly when the mosses are growing in comparable environments.