The Almofront-2 cruise (22 November 1997 – 18 January 1998) was aimed at documenting physical, chemical and biological characteristics of the Alboran Sea. Both horizontal and vertical distributions of picophytoplankton (Prochlorococcus spp., Synechococcus spp. and small photosynthetic eukaryotes), heterotrophic prokaryotes and viruses were investigated using flow cytometry (FCM). Three types of ecosystems were discriminated on the basis of physical parameters and picoplankton distribution: the Mediterranean ecosystem (MED) in the Northern part, the anticyclonic gyre of modified Atlantic (ATL) water in the southern part, and the frontal ecosystem in between. MED waters were dominated by Prochlorococcus while Synechococcus concentration was higher in ATL waters. High concentrations of both groups were also recorded in dense waters of the front, a likely response to nutrient injection from deeper and/or adjacent waters. Photosynthetic picoeukaryotes concentration was the highest in regions influenced by the front and at the periphery of the gyre. The low biomass of picoeukaryotes in dense waters of the front suggests that this group responded very differently to environmental factors compared to Prochlorococcus and Synechococcus. Picoplankton contributed up to 50% of total chlorophyll a (Chl a) in the gyre (mean ca 25%), essentially due to the picoeukaryotes. The biomass of the picophytoplankton clearly decreased between the two legs. Heterotrophic bacteria concentrations were well correlated to those of picoeukaryotes and reached their maximum in the central part of the Alboran eastern gyre. Two patches of high concentration of heterotrophic bacteria were recorded in frontal-influenced MED waters and were tightly coupled to maximal Chl a concentrations following the 28.1-28.2 density excess isolines. At this period of the year, picoplankton could represent up to 50% of the <200 μm living organic carbon in MED waters and up to 35% in modified ATL waters (mean 35 and 23%, respectively). At last, two groups of virus-like particles (VLPs) were discriminated by FCM according to DNA content fluorescence. No major differences in their distribution patterns were recorded between sites. A significant correlation was found between heterotrophic bacteria numbers and VLPs suggesting a tight coupling between the two communities. In conclusion, picoplankton appears to constitute an important fraction of living matter in the Alboran Sea at the end of fall and early winter and may thus participate significantly to carbon and energy fluxes in the W. Mediterranean Sea.