The Vlora Bay is the only internal sea of the Albanian coastline. The site is of paramount interest for Albanian fishing, being a natural nursery for many fish species of economic importance. The composition of the plankton community in the Vlora Bay has been analysed and particular attention devoted to the unicellular eukaryotes by collecting samples from 16 stations during 2 seasonal cruises (May–June 2007, and January 2008), an effort to date never carried out to know the plankton biodiversity of the area.

The microzooplankton community was composed of 122 phytoplankton and 105 microzooplankton taxa, of which 58.2% and 25.0%, respectively, were classified as seasonal (they were recorded only in one of the two considered times). Only four categories (all phytoplanktonic, the diatom Navicula sp., “undetermined naked dinoflagellates < 15 µm”, the coccolithophorid Emiliania huxleyi, and the “undetermined phytoflagellates < 10 µm”) were recorded in all the sampling stations (at least in one period). The microzooplankton were particularly diversified and characteristic in their Ciliophora components.

A statistical analysis of taxa distribution allowed us to identify three distinct areas in the Vlora Bay: internal, intermediate, and external. The extension or the border position of these areas varied with the seasons and according to the microzooplankton group examined. The microzooplankton assemblages of the Vlora Bay showed significant differences with many other sites in the Mediterranean Sea, probably due to the crucial geographic position the bay occupies among different Mediterranean basins.