Abstract In this study, we investigate the occurrence of primary biological aerosol particles (PBAP) over all sectors of the Southern Ocean (SO) based on a 90‐day data set collected during the Antarctic Circumnavigation Expedition (ACE) in austral summer 2016–2017. Super‐micrometer PBAP (1–16 µm diameter) were measured by a wide band integrated bioaerosol sensor (WIBS‐4). Low (3σ) and high (9σ) fluorescence thresholds are used to obtain statistics on fluorescent and hyper‐fluorescent PBAP, respectively. Our focus is on data obtained over the pristine ocean, that is, more than 200 km away from land. The results indicate that (hyper‐)fluorescent PBAP are correlated to atmospheric variables associated with sea spray aerosol (SSA) particles (wind speed, total super‐micrometer aerosol number concentration, chloride and sodium concentrations). This suggests that a main source of PBAP over the SO is SSA. The median percentage contribution of fluorescent and hyper‐fluorescent PBAP to super‐micrometer SSA was 1.6% and 0.13%, respectively. We demonstrate that the fraction of (hyper‐)fluorescent PBAP to total super‐micrometer particles positively correlates with concentrations of bacteria and several taxa of pythoplankton measured in seawater, indicating that marine biota concentrations modulate the PBAP source flux. We investigate the fluorescent properties of (hyper‐)fluorescent PBAP for several events that occurred near land masses. We find that the fluorescence signal characteristics of particles near land is much more variable than over the pristine ocean. We conclude that the source and concentration of fluorescent PBAP over the open ocean is similar across all sampled sectors of the SO.