During a research expedition to the Northwest Pacific between July 13 and August 11, 2019, we collected oceanic zooplankton samples over the Emperor Seamounts (Koko, Jingu, Nintoku, and Suiko guyots). We analyzed the horizontal and vertical distributions of abundance and biomass and also the structure of the zooplankton in the highly productive but poorly studied ocean waters between 34° and 44° N. The zooplankton was represented by four genera of amphipods, seven genera of pteropods, 39 genera of copepods, and larvae of benthic invertebrates and fish. The abundance and biomass of zooplankton increased towards higher latitudes along the series Koko < Jingu < Nintoku < Suiko guyots. The highest index of diversity was recorded over the Koko and Jingu guyots; the highest species richness occurred over the Jingu and Nintoku guyots. Small-sized copepods, appendicularians, chaetognaths, euphausiids, and fish eggs and larvae concentrated in the epipelagic; large copepods and ostracods concentrated in the mesopelagic. We identified three types of zooplankton assemblages: a Subtropical assemblage between 34°–35° N characterized by tropical/subtropical forms; a Transition assemblage characterized by subtropical, subarctic, and widespread species between 38°–41° N; and a Subarctic assemblage characterized by subarctic and widespread species between 43°–44° N. The spatial distribution of zooplankton was a function of environmental variables such as surface salinity, temperature at 200-m, and, to a certain extent, by surface Chl-a concentrations.