The interacting features of topography and hydrography around deep seamounts have strong influence on plankton biogeography. In addition, the intrinsic properties of various biological taxa inherently shape their distribution. Therefore, bacterial, protist and fungal diversity was investigated across the water column above and below the summit of a flat-topped seamount in the Western Pacific Ocean. We determined the distribution and connectivity patterns of bacteria, protists and fungi around the seamount, and explored the processes driving the observed distribution patterns. We found that the seamount enhanced the vertical connectivity of bacterial and protist communities, but significantly reduced the protist community connectivity along the horizontal dimension. Such effects provide ecological opportunities for eukaryotic adaption and diversification, resulting in a greater diversity on seamounts than in surrounding deep seas.