Isoprene produced by marine phytoplankton acts as a precursor of secondary organic aerosol and thereby affects cloud formation and brightness over the remote oceans. Yet, the marine isoprene emission is poorly constrained, with discrepancies among estimates that reach 2 orders of magnitude. Here we present ISOREMS, the first satellite-only based algorithm for the retrieval of isoprene concentration in the Southern Ocean. Sea surface concentrations from six cruises were matched with remotely-sensed variables from MODIS Aqua, and isoprene was best predicted by multiple linear regression with chlorophyll-a and sea surface temperature. Climatological (2002-2018) isoprene distributions computed with ISOREMS revealed high concentrations in coastal and near-island waters, and within the 40º-50ºS latitudinal band. Isoprene seasonality paralleled phytoplankton productivity, with annual maxima in summer. The annual Southern Ocean emission of isoprene was estimated 61 Gg C yr $\mathrm{^{-1}}$. The algorithm can provide spatially and temporally realistic inputs to atmospheric and climate models.