Symbiosis is a ubiquitous form of evolutionary innovation that has shaped countless complex biological systems and specialised mutualistic relationships represent a rich source of natural products. These compounds can be specialised molecules, called secondary metabolites, that are evolutionary refined to give the producing organisms a competitive advantage in their current environment. Signalling and defence interactions between organisms play central roles in shaping the chemistry within symbiosis and bacterial and fungal symbionts have shown enormous novel chemistry with huge potential for application. Fungus-farming termites of the subfamily Macrotermitinae form a 30-million-year-old mutualistic relationship with their gut microbiome and the basidiomycete fungus Termitomyces. The insects provide plant substrates and maintain an internal nest microenvironment that is favourable for their fungus symbiont, which in turn provides a nutritious food source for the termite hosts. Despite the fungal cultivar being maintained in a monoculture and the termites foraging in pathogen rich environments, this symbiosis shows an exceptional capacity to keep their valuable fungus-comb free from antagonists. The work of this thesis aims to enrich our knowledge of natural products from the fungus- growing termite symbiosis and elucidate defensive roles with particular focus Termitomyces. In Chapter 1, we compiled all previously studied natural product production from all members of the symbiosis, to demonstrate that compound from termite, bacterial and fungal symbiont contain bioactivity that can contribute to nest defence and that the natural product discovery potential from the symbiosis remains massive as only a small fraction has been explored. In Chapter 2, we identified the best-suited optimal DNA extraction protocol for long read sequencing, as high-quality DNA is essential to accurately predict biosynthetic gene clusters (BGCs) encoding secondary metabolites. Next, we investigated the chemical potential of the fungal symbiont from 21 Termitomyces species and identified BGCs in an evolutionary context. This allowed us to show that Termitomyces species and termite host significantly affect the biosynthetic diversity, and that some BGCs are under positive selection. These analyses further indicated that the vast majority of the BGCs are likely to code for yet-to-be characterised natural products. In Chapter 4, we showed that the termite guts harbour complex metabolomics distinguishable by termite species and castes. This is dominated by primary metabolites that likely are a product of nutrition, but the metabolite profiles also included a small number of bioactive compounds with proposed microbial origin that could be defensive. In Chapter 5 we took a closer look at the extended phenotype that is the termite mound in defence, by showing that elevated CO2 levels has the ability to act as an additional protective barrier that minimises the growth of fungal contaminants. Collectively, this thesis demonstrates that the fungus-growing termite symbiosis harbours a huge unexplored chemical potential and the possibility for novel compound discovery. The bioactive activity from all partners of the symbiosis along with the harsh internal environment of the mound most likely contribute complementary defensive functions in the symbiosis where maintain enclosed homeostasis is critical to sustain the fungal garden health.