This study investigates this smallest plankton fraction (cells ≤ 3µm) in both prokaryotic and eukaryotic perspective considering changes of the community in the photic zone from coastal to open sea during mixed winter conditions. Using high-throughput sequencing of 16S and 18S rRNA genes along with flow-cytometry counts of bacteria, cyanobacteria and photosynthetic picoeukaryotes (PPEs) we described picoplanktonic community in the oligotrophic ecosystem. With pigment and lipid analyses of picoplankton community, we characterized PPEs and detected specific events in microbial loop. Prokaryotic community was dominated by Alphaproteobacteria, mainly SAR11 clade (44.91%), followed by Gammaproteobacteria (Oceanospirillales and Pseudomonadales, 14.96%), Bacteroidetes, mainly Flavobacteriales (13%), Cyanobacteria (Prochlorococcus and Synechococcus, 9.52%), Marinimicrobia, SAR406 clade (7.97%), Deltaproteobacteria (3.83%), Actinobacteria (2.24%) and Chloroflexi (1.90%). Picoeukaryotes, although the drivers of photosynthetic activity in oligotrophic systems, in this study were dominated by heterotrophic counterparts: Syndiniales, parasitic dinoflagellates (79.67%), other Dinophyta (8.7%) and on two depths Collodaria, family Sphaerozoidae (22.1%) and Polycistinea, Spumellarida (5.0%), while total photoautotrophic fraction of picoeukaryotes were represented with Mamiellophyceae, Stramenopiles, photoautotrophic Cryptophyta and some Haptophyta, together not exceeding 5% of total sequences. Heterotrophic bacteria and cyanobacteria, separated into populations of Prochlorococcus and Synechococcus, had abundances up to 7×105; 2.3×104 and 2.5×104 cells mL-1, respectively. Photoautotrophic picoeukaryotes were most abundant at P600-25m with 3×103 cells mL-1. According to pigment composition, the most prevalent phototrophs in picoplankton were Cyanobacteria and green algae.