Two coarse suspended matter size classes (75–150 μm, >150 μm), from subantarctic and Antarctic surface waters in the Scotia Sea, and sediment trap material from the Drake Passage were analyzed for their elemental, amino acid and amino sugar compositions. Different proportions of biogenic silica and organic matter in the particulates of both regions reflect a zonation of primary producers, with diatoms predominating in the waters south of the Polar Front. High SiO 2:C org ratios, elevated proportions of hydroxyl amino acids, and essentially identical amino acid compositions for both size classes indicate that diatoms account for a major portion of the particulate proteinaceous material from Antarctic surface waters. Of the two amino sugars, glucosamine and galactosamine, only the former was detected in significant amounts in the surface particulates. The total amino acid : glucosamine ratio was lowest in surface particulates of subantarctic waters and increased with increasing latitude in Antarctic waters, reaching the highest values in the region of the Bransfield Strait. Moreover, amino acid : glucosamine ratios suggest day-night differences in particulate matter resulting from primary productivity in conjunction with the feeding behavior of vertical migrators. Significantly different amino acid and amino sugar compositions of the surface particulate matter >75 μm in size and the sediment trap material reflect fractionation processes at shallow depths. Remineralization and digestion of organic matter appear to result in a relative enrichment of structural components (diatom cell walls, chitinaceous matter) in fecal pellets and other large aggregates. The preferential preservation of diatom cell wall material is indicated by a strong relative enrichment of glycine and hydroxyl amino acids in the sediment trap material in conjunction with high biogenic silica:organic carbon ratios. Similarly, low amino acid:glucosamine ratios in the sediment trap material from depths point to a preferential preservation of chitinaceous matter. Slight compositional differences between the material from the upper and lower trap may indicate that bacteria are acting on the rapidly sinking particles. These changes appear to be insignificant, however, when compared to the fractionations occurring at shallow depths.