The Okinawa Backarc Basin sediments encompass spatial diversity of physical and geochemical inputs from the subsurface hydrothermal network of the Iheya North Hydrothermal Field. Previous microbial community gene-based assessments reflect stratified and diverse communities of Bacteria and Archaea between cored IODP Expedition 331 sites. Furthermore, temperature constrains in sediments affected by hydrothermal fluid flow (Site C0014) restrict the biosphere to the upper meters of sediments. In this study, we attempt to supplement the gene-based and metagenomic studies from Sites C0014 (heated sediments) and C0017 (recharge zone sediments) with an RNA-based approach to selectively investigate the active microbial populations. The results from sequenced reverse transcribed 16S rRNA demonstrate the sensitivity of extraction and amplification to external nucleic acids and attest to the challenges in working with low biomass environmental samples, but may also reveal certain bacterial taxa (e.g. Bacteroidetes and Alphaproteobacteria) recovered from select sediment horizons. However, inconsistencies between primer sets and replicates make conclusions about the results of this RNA study extremely tenuous.