In the bathypelagic realm of the ocean, the role of marine snow as a carbon and energy source for the deep-sea biota and as a potential hotspot of microbial diversity and activity has not received adequate attention. Here, we collected bathypelagic marine snow by gentle gravity filtration of sea water onto 30 μm filters from ~1000 to 3900 m to investigate the relative distribution of eukaryotic microbes. Compared with sediment traps that select for fast-sinking particles, this method collects particles unbiased by settling velocity. While prokaryotes numerically exceeded eukaryotes on marine snow, eukaryotic microbes belonging to two very distant branches of the eukaryote tree, the fungi and the labyrinthulomycetes, dominated overall biomass. Being tolerant to cold temperature and high hydrostatic pressure, these saprotrophic organisms have the potential to significantly contribute to the degradation of organic matter in the deep sea. Our results demonstrate that the community composition on bathypelagic marine snow differs greatly from that in the ambient water leading to wide ecological niche separation between the two environments.The ISME Journal advance online publication, 20 September 2016; doi:10.1038/ismej.2016.113.