Secondary metabolites are widespread among lower phyla and understanding their functional role(s) in the producing organism has been under study in recent decades. Considerable progress has been made in understanding chemical ecological interactions among terrestrial organisms, and similar research in the marine realm has been initiated in recent years. Polar regions are more difficult to access and thus progress has been slower. Nevertheless, the extreme and often unique marine environments surrounding Antarctica as well as the many unusual trophic interactions in antarctic marine communities might well be expected to select for novel secondary metabolites and/or novel functional roles for secondary metabolites. Indeed, recent studies have documented novel, chemically-mediated interactions between molluscs and amphipods, between algae, urchins and anemones, and between sponges and their predators. The Porifera are the dominant phylum on the McMurdo Sound benthos, and representatives of this phylum have been shown to elaborate sea star feeding deterrents, inhibitors of fouling or infectious organisms, and metabolites which mediate predation via molt inhibition. As a result of studies on Antarctic sponges, new insights into functional roles of pigments and the ability of sponges to sequester metabolites have been gained, and a new mechanism of chemical defense has been described. Herein we describe recent results of our studies of trophic interactions between sponges and their predators that are mediated by specific sponge secondary metabolites. Moreover, we highlight unusual chemically-mediated interactions in antarctic marine invertebrates other than sponges.