Sponges are known to be a rich source of structurally diverse bioactive natural products, accounting for approximately one third of the 25,000 novel marine natural products discovered to date. The advancement of molecular techniques, especially next generation sequencing, has revealed a highly diverse and complex microbial consortia associated with sponges. Currently, research is on-going to investigate the role of these microorganisms in symbiosis and in the production of these sponge-associated secondary metabolites. It is hypothesised that adaptations to extreme temperatures and oxygen levels in the Antarctic may result in novel microbial strains with unprecedented bioactive metabolites. Although ecological and environmental factors are believed to play a crucial role in the expression of microbial bioactive secondary metabolites, underpinning the ecological function of microorganism- sponge interactions within Antarctica is poorly understood, despite mounting evidence that these metabolites play an important role in chemical defence and microbial community structure. The importance of the Antarctic ecosystem as a research resource will be underpinned by future global change; therefore it will be vital for ecological approaches to be addressed in addition to these biomedical functions. This review collates studies that assess the biomedical activity of secondary metabolites produced by Antarctic sponge associated microorganisms, which may stimulate the ecological function to be addressed by the community.