Marine microorganisms play a crucial role in biogeochemical cycles, especially in the surface microlayer (SML), which differs from adjacent subsurface waters (SSW). In this study, we sampled the SML and SSW at 20 sites along the western Antarctic Peninsula during the summers of 2015 and 2019, examining microbial, viral and environmental differences. We focused on phototrophic protists, specifically Phaeocystis-like species, known for their high dimethylsulphoniopropionate (DMSP) contents, which can be released through viral lysis. DMSP is a precursor to dimethylsulphide (DMS), a gas influencing Earth’s climate. We hypothesized a significant relationship between Phaeocystis-like abundance and DMSP concentration, with strong interactions with their specific viruses (V4) in the SML. Most biotic variables showed higher mean values in the SML, although these differences often were not statistically significant. DMSP concentrations correlated with Phaeocystis-like species abundance in both layers (R2 = 0.482, P ≤ 0.01; R2 = 0.532, P ≤ 0.01, respectively), whereas V4 abundance significantly correlated with Phaeocystis-like species only in the SML (R2 = 0.572, P ≤ 0.01). These results suggest stronger interactions between viruses and DMSP-rich hosts in the SML, potentially increasing DMS emissions to the atmosphere and impacting climate regulation.