Foraminifera are adapted to a wide range of environments from the surface ocean to the sea floor and are even found in freshwater. Here, we used eDNA metabarcoding to evaluate seasonal changes in benthic and planktic foraminiferal communities identified in seawater and sediments collected in June and August around the Takuyo-Daigo Seamount. Our seawater samples contained a moderate amount of eDNA from benthic foraminifera, which may be attributed to the presence of suspended particles transported by deep-sea flow. Rough seasonal shifts in the planktic foraminiferal assemblages can be seen in seawater samples. Among benthic foraminifera, monothalamids were the most common, as has been found in other deep-sea regions. Our results suggest that depth within the sediment can affect the composition of benthic foraminifera, but the timing of collection did not have a strong influence on benthic assemblages.