<p>Understanding the seasonal variations of the zooplankton community’s structure in the Western Pacific Warm Pool (WPWP)—the most stable open marine environment in the Pacific Ocean—is crucial to predict the impacts of climate change on the ecosystem. However, knowledge on these variations in this region down to the mesopelagic zone is insufficient. In this study, the environmental DNA (eDNA) metabarcoding method was used to investigate the zooplankton community during summer, autumn, and winter, from the surface to a depth of 1 000 m spanning the epipelagic to mesopelagic zones. The zooplankton community structure exhibited seasonal fluctuations at multiple depths except for 200 and 1 000 m. In addition, a stronger zooplankton seasonality was particularly recorded in the epipelagic zone than in the mesopelagic zone, which is consistent with the environmental changes. The studied zooplanktons are dominated by medusae and copepods that showed distinct seasonality. At all depths, medusae exhibited greater seasonal variations than the overall zooplankton community, whereas the copepods did not exhibit significant seasonality. The environmental features and the seasons exerted greater influences on the structure of the zooplankton communities than did the spatial factors. The results of this study indicate that eDNA metabarcoding can provide novel insights into zooplankton assemblages due to its ability to capture a rich variety of medusae, which are often underestimated by net collection.</p>