We compared seasonal feeding habit patterns, mouthpart structures, body sizes and vertical distributions of the aetideid copepods Undeuchaeta major and Chirundina streetsii in Sagami Bay, Japan. We focused on niche partitioning as one of the mechanisms sustaining coexistence of these mesopelagic copepods, by integrative application of stable-isotope analysis, microscopic observation and elemental analysis of the gut contents. While the body sizes and vertical distribution of both species were similar, they showed marked differences in their feeding habits throughout the year, i.e. carnivory in U. major and omnivory in C. streetsii, suggesting that food niche partitioning was a mechanism enabling their co-existence. Of particular interest was the consistently lower δ 15 N values in U. major, attributable to its selective feeding on oncaeid copepods. Previous reports of low δ 15 N in oncaeids, whose major food source has been assumed to be nanoplankton attached to appendicularian houses, suggest that the size of the primary producer is important in δ 15 N analyses of pelagic food webs. Comparison of mouthparts of the 2 species indicated slight differences in the maxilliped morphology. The relationship between feeding habit and maxilliped morphology was examined for the species above, other omnivorous aetideids and the Euchaetidae, a carnivorous sister family of the Aetideidae. The results suggest that carnivores have a broad basis and long unguiform setae, while omnivores have a narrower basis and shorter, more slender setae. The feeding habits of Aetideidae, which have so far been considered as exclusively omnivorous, comprise omnivory and carnivory, and can be distinguished by their maxilliped morphology.