The diversity and distribution of epipelagic metazooplankton across the Mediterranean Sea was studied along a 3000 km long transect from the eastern to the western basins during the BOUM cruise in summer 2008. Metazooplankton were sampled using both a 120 mu m mesh size bongo net and Niskin bottles in the upper 200 m layer at 17 stations. Here we report on the stock, the composition and the structure of the metazooplankton community. The abundance was 4 to 8 times higher than in several previously published studies, whereas the biomass remained within the same order of magnitude. An eastward decrease in abundance was evident, although biomass was variable. Spatial (horizontal and vertical) distribution of metazooplankton abundance and biomass was strongly correlated to chlorophyll-a concentration. In addition, a clear association was observed between the vertical distribution of nauplii and small copepods and the depth of the deep chlorophyll maximum. The distinction between the communities of the eastern and western basins was clearly explained by the environmental factors. The specific distribution pattern of remarkable species was also described.