Vertical distribution of zooplankton species is controlled by physical parameters and thus affects predator-prey relationships and hence trophic interactions. Fish and gelatinous plankton often feed in distinct layers or show feeding migrations. Both temporal and spatial match are required for successful predation. Here we present data on the seasonal and vertical distribution of dominant zooplankton species in the Bornholm Basin (Central Baltic Sea) from 15 cruises between March 2002 and May 2003. Multinet hauls were taken in 10m intervals from bottom to surface and correlated with CTD data. The dominant crustaceans were grouped to four main patterns which correlated with physico-chemical parameters. While in most copepods the whole population showed a distinct seasonal vertical distribution pattern, in other species vertical distribution was ontogenetically different. The cladoceran Bosmina, dominating during the warm periods, preferred mainly the upper, warm stratified water column. Species adapted to cooler water, like Evadne nordmanni, seem to use the thermocline as a retreat area during summer. Our data implicate that in the Baltic Sea the thermocline and halocline are key features for vertical distribution; in addition the thermocline itself could represent a habitat for several species or their offspring.