Acoustic surveys in the vicinity of the sub-Antarctic island of South Georgia revealed the existence of a number of horizontally extensive yet vertically discrete scattering layers in the upper 250 m of the water column. These layers were fished with a LonghurstHardy plankton recorder (LHPR) and a multiple-opening 8 m2 rectangular mid-water trawl (RMT8). Analysis of catches suggested that each scattering layer was composed predominantly of a single species of either the euphausiids Euphausia frigida or Thysanöessa macrura, the hyperiid amphipod Themisto gaudichaudii, or the eucalaniid copepod Rhincalanus gigas. Instrumentation on the nets allowed their trajectories to be reconstructed precisely, and thus catch data to be related directly to the corresponding acoustic signals. Discriminant function analysis of differences between mean volume backscattering strength at 38, 120 and 200 kHz separated echoes originating from each of the dominant scattering layers, and other signals identified as originating from Antarctic krill Euphausia superba, with an overall correct classification rate of 77%. We therefore demonstrate that with the use of echo intensity data alone, gathered using hardware commonly employed for fishery acoustics, it is possible to discriminate in situ between several zooplanktonic taxa, taxa which in some instances exhibit similar gross morphological characteristics and have overlapping length-frequency distributions. Acoustic signals from the mysid Antarctomysis maxima could additionally be discriminated once information on target distribution was considered, highlighting the value of incorporating multiple descriptors of echo characteristics into signal identification procedures. The ability to discriminate acoustically between zooplankton taxa could usefully be applied to provide improved acoustic estimates of species abundance, and to enhance field studies of zooplankton ecology, distribution and species interactions.