Marine zooplankton are among the most diverse and abundant organisms on earth. Despite a great wealth of knowledge and research on their ecology, the processes promoting coexistence and maintaining their high diversity worldwide are poorly known. In order to understand the processes underpinning coexistence among marine zooplankton, we investigated the existence and degree of niche separation within two pairs of taxonomically and ecologically related species of copepods belonging to the widespread, abundant genera Calanus and Oithona. We compared the spatial variation in species abundances to the abiotic and biotic environment using a multimodel approach and vertically resolved survey data on zooplankton composition, abundances, and environmental conditions in the North Sea. Our results demonstrate pronounced spatial differences between species in each pair, primarily in their vertical abundance distributions. These differences can largely be explained by different preferences for temperature and salinity. This supports the occurrence of environmental niche separation in marine zooplankton and highlights its role as a mechanism reducing interspecific competition and promoting coexistence.