We compared stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) of epi- and mesopelagic mesozooplankton communities at subarctic (K2) and subtropical (S1) sites in the North Pacific Ocean to evaluate the relationship between mesopelagic communities and epipelagic production. Although δ13C and δ15N varied among the taxonomic groups, ostracods, carnivorous copepods, and chaetognaths tended to exhibit higher δ13C and δ15N than omnivorous copepods within the same layers. Mesozooplankton δ13C and δ15N were higher in the upper (200–500 m) and lower (500–1000 m) mesopelagic layers than in the epipelagic layer (0–150 m). δ13C and δ15N of mesozooplankton were positively correlated at all three depth-ranges at both sites. Although the slopes of linear regressions of δ15N vs. δ13C exhibited no significant differences among layers or between sites, the intercept was lower for mesozooplankton at S1. We attributed the similarity of slopes to common isotopic fractionation during protein synthesis among the different taxonomic groups, and the lower intercept to primary producers supported by recycled nutrients and atmospheric nitrogen fixation under the high thermal regime at S1. Our results further confirm earlier evidence that metabolic requirements of mesopelagic communities are supported by epipelagic production through the biological pump.