A suite of molecular methods targeting 16S rRNA genes (i.e., DGGE, clone and high-throughput[HTP] amplicon library sequencing) was used to profile the microbial communities in deep Fennoscandiancrystalline bedrock fracture fluids. Variation among bacterial 16S rRNA genes was examinedwith two commonly used primer pairs: P1/P2 and U968f/U1401r. DGGE using U968f/U1401r mostly detected β-, γ-proteobacteria and Firmicutes, while P1/P2 primers additionallydetected other proteobacterial clades and candidate divisions. However, in combination withclone libraries the U968f/U1401r primers detected a higher bacterial diversity than DGGE alone.HTP amplicon sequencing with P1/P2 revealed an abundance of the DGGE bacterial groups as wellas many other bacterial taxa likely representing minor components of these communities. Archaealdiversity was investigated via DGGE or HTP amplicon sequencingusing primers A344F/519RP. The majority of archaea detected with HTP amplicon sequencing belonged to unculturedThermoplasmatales and Pendant 33/DHVE3, 4, 6 groups. DGGE of the same samples detectedmostly SAGMEG and Methanosarcinales archaea, but almost none of those were revealed by HTPamplicon sequencing. Overall, our results show that the inferred diversity and composition of microbialcommunities in deep fracture fluids is highly dependent on analytical technique and thatthe method should be carefully selected with this in mind.