A distinctive assemblage of epiphytic diatoms is recovered from Neogene Southern Ocean abyssal sediments, far removed from shallow coastal waters where they are important elements of coastal benthic ecosystems. Epiphytic diatoms maintained a position in the euphotic zone attached to buoyant macroalgal (seaweed) rafts. The stratigraphic occurrence of large, benthic epiphytic diatoms of genera Arachnoidiscus, Isthmia, Rhabdonema, Gephyra, Trigonium, and smaller Achnanthes, Cocconeis, Grammatophora, and Rhaphoneis in sediment cores from Southern Ocean abyssal plain reflects times when macroalgae were abundant in the Southern Ocean. The discontinuous stratigraphic occurrence of the epiphytes (often exceeding 10% of the total diatom flora) amongst the background of planktonic diatoms suggests environmental changes induced by either warm or cold events that controlled the production and/or release of the macroalgae and their attached epiphytes into the deep-sea. Well-resolved climate cycles in IODP Site U1356 (Pliocene) and Site U1361 (Miocene) help to develop this new proxy to identify times when floating macroalgal oases were an important feature of the ‘pelagic’ Southern Ocean realm, and helped deliver organic material to the deep sea. Macroalgae attach to coastal substrates with a holdfast, a multi-fingered structure that serves as an anchor and can raft large sedimentary particles into the deep-sea. Amphipods thrive in this community, grazing epiphytic diatoms and producing diatom-rich fecal pellets that sink rapidly to the abyssal seafloor. The epiphytic diatom occurrences offer an opportunity to develop a new paleobiological proxy to interpret Antarctic paleoenvironmental history, specifically to: (1) provide insight into Neogene extent of open marine shelves on the Wilkes Land margin; (2) infer intervals of substantial Neogene ice sheet retreat from interior Antarctic basins; (3) reassess interpretations of terrigenous sediment grains in the deep-sea, inferred previously to result from iceberg-rafting in the Southern Ocean that may also result from biological rafting; and (4) consider the timing for paleobiogeographic dispersal of invertebrate organisms living within macroalgal holdfast communities to Subantarctic islands.