The spatio-temporal patterns of a zooplankton community structure in a strongly stratified enclosed marine environment were studied over a one-year period. Copepods were by far the most abundant group, accounting for 69-91% of the total zooplankton, with a numerical dominance of the genus Oithona. Cluster analysis revealed four different groups of samples and a comparison was made of the hydrographical and biological properties of the resulting groups. Water temperature was the main force discriminating the zooplankton community. The strongest vertical separation was recorded in summer, while a salinity impact was noted during the autumn after a strong intrusion of open sea water. Most of the dominant zooplankters exhibited a distinct vertical separation over the study period, where thermophilic taxa (Cladocera, Centropages kröyeri, C. typicus, Oikopleura fusiformis, O. longicauda, Euterpina acutifrons) kept to the surface and cryophilic species (Diaixis pygmaea, Mesaiokeras hurei, Calanus helgolandicus, Parasagitta setosa) were concentrated below the thermocline layer (20 m depth) for most of the year. Due to the unique physical, chemical and biological properties of the study site, this research is an important step towards better understanding the distribution of zooplankton during stratified conditions.