Summary Studies on the microbial communities of deep subsurface sediments have indicated the presence of Bacteria and Archaea throughout the sediment column. Microbial eukaryotes could also be present in deep‐sea subsurface sediments; either bacterivorous protists or eukaryotes capable of assimilating buried organic carbon. DNA‐ and RNA‐based clone library analyses are used here to examine the microbial eukaryotic diversity an...