The current study address microbial diversity of Alpine bog vegetation using deep-sequencing of microbial 16S rRNA genes. Higher plant, bryophyte and lichen species were sampled from plots (1m2) in two Austrian bogs, Rotmoos and Pürgschachen Moor. The plots were dominated by Sphagnum magellanicum or Sphagnum angustifolium. Altogether, 46 plant and lichen samples of 24 species were collected. Amplicons were generated using 515F/806R (Caporaso et al. 2010 PNAS) and were sequenced using Illumina MiSeq v2 platform.