Despite their size, prokaryote (bacteria and archaea) biomass is estimated to represent between 15 and 30% of total living biomass1,2. Prokaryotes play major roles in marine ecosystems and in global biogeochemical cycling3,4. Molecular phylogenetic approaches have revolutionised microbiology and have revealed that the complexity of microbial life is orders of magnitude greater than previous estimates based on cultivation-based approaches5. This highlights how little we currently know about the microbial world and the clear potential of this vast untapped resource for human application. Here we present the first in-depth analysis of microbial community diversity and composition in the Irish Sea. The western Irish Sea is characterised by distinct hydrographic conditions, resulting in summer stratified offshore deeper waters and settling of fine mud, while well-mixed waters and coarser sediment type dominate in the south and coastal regions. We wished to assess whether these factors play a role in prokaryote abundance and diversity.