Seasonal changes in diversity and community structure of planktonic copepods at a shelf site in Sagami Bay, Japan was studied in relation to cross-shelf interaction of species components. Seasonal mesozooplankton samples were collected from the shelf station (St. M) of the north-west part of Sagami Bay from 1995 to 1997. Vertical multi-layered samples were collected near the center of Sagami Bay (St. P) in June 1996. A total 185 copepod species were identified from the two stations. We observed a clear seasonal succession in calanoid diversity and community structure at St. M from a simple shelf water community (>11 species) during spring blooming periods to highly diverse and mixed communities (ca 20–30 species) of shelf water species coupled with various Kuroshio Current species during late summer to autumn. Cluster and non-metric multidimensional scaling ordination analyses showed two distinct calanoid community groups. One group, which included samples of St. M and the surface layer of St. P, consisted of shelf water species, such as Calanus sinicus, Ctenocalanus vanus, Paracalanus spp., and Kuroshio species, such as, Canthocalanus pauper, Scolecithrix danae, etc. The other cluster was restricted to the samples collected from mid and deep layers at St. P, which consisted of meso- and bathypelagic species and Oyashio species (cold-current species, such as Neocalanus cristatus, Pseudocalanus spp., Eucalanus bungii and Metridia pacifica). In the mid and deep layers at St. P, the population of dormant copepodid stage V (CV) of Eucalanus californicus and C. sinicus were dominant. The deep CV population of C. sinicus might be ecologically discriminated from the surface and shelf water population due to their larger body length and dormant life cycle. E. californicus was also collected at the shelf site during each spring bloom period, whereas the population might descend into the mid- and deep-layers of the central bay before summer. Our results suggest that the seasonal fluctuation of community structure in the shelf water was controlled by both physical (Kuroshio Current) and biological factors, i.e., spring bloom and ontogenetic vertical migration of E. californicus. In particular, transport and diffusion processes of Kuroshio Current in Sagami Bay played a key role in controlling the shelf water calanoid community.