Marine ecosystems are important drivers of the global climate system. They emit volatile species into the atmosphere, involved in complex reaction cycles that influence the lifetime of greenhouse gases. Sea spray and marine biogenic aerosols affect Earth’s climate by scattering solar radiation and controlling cloud microphysical properties. Here we show larger than expected marine biogenic emissions of butenes, three orders of magnitude higher than dimethyl sulphide, produced by the coastal part of the Benguela upwelling system, one of the most productive marine ecosystems in the world. We show that these emissions may contribute to new particle formation in the atmosphere within the marine boundary layer through production of Criegee intermediates that oxidise SO2 to H2SO4. Butene emissions from the marine biota may affect air quality and climate through ozone, secondary organic aerosol, and cloud condensation nuclei formation even in pristine regions of the world. Our results indicate a potentially important role of butene emissions in marine particle formation that requires investigation in other regions.