Microorganisms are ubiquitous and highly diverse in the atmosphere. Despite airborne bacteria over the Southern Ocean (SO) potentially impact to ecology in isolated Antarctica (barrier and source) and climate (cloud formation), no previous region-wide assessment of bioaerosols over the SO has been reported. To understand latitudinal variations in airborne bacterial communities and to use source tracking to deduce sources of the bacterial communities, we investigated bacterial profiling from air filter samples taken during CAPRICORN-2018 cruise.