ABSTRACT: Phenological changes in microalgal production and community structure are occurring in the Arctic Ocean. In particular, delayed sea ice formation in autumn can extend the microalgal growth season; however, the succession of phytoplankton communities during this longer photoavailable season is poorly understood. Our objective is to relate oceanographic conditions to the variability in total phytoplankton biomass by examining diatom assemblages in the Chukchi Sea during autumn. We combined scanning electron microscopy (SEM) and DNA metabarcoding techniques to characterize diatom communities, including resting spores of the genus Chaetoceros. The upper layer from the shelf slope to the basin is generally well stratified and influenced by sea ice meltwater. This stratification prevents the supply of nutrients from the lower layers; therefore, the diatom community is characterized by the typical autumn diatom genus Proboscia near the surface. On the southern shelf, the wind modulated the bottom current, and in turn, the current induced the resuspension of sediments and microalgae. Therefore, we speculate that strong winds enhanced the currents within the benthic boundary layer, which entrains Chaetoceros resting spore-rich sediments and nutrients (including NH4) to the ocean interior, resulting in a seeding potential for autumn phytoplankton blooms. Multiple data from the cruise and the moorings suggested that the resuspension of sediments and microalgae could commonly occur in the shelf during autumn. The enhanced wind activity in the shallow Chukchi Sea could be important for biogeochemical processes by facilitating the supply of nutrients and viable diatoms from the seafloor to the upper water column.