Little is known about the taxonomic and phylogenetic diversities, and the relative importance of historic processes and environmental gradients underlying the current diversity and community assembly, of single-celled eukaryotes in marine benthic habitats. By pyrosequencing ribosomal RNA genes and characterizing multiple environmental factors, we investigated temporal and spatial patterns of a- and ß-diversities of microeukaryotes in near-surface sediments of three basins of the Yellow Sea Large Marine Ecosystem.