The aim of my PhD was to examine the microbial communities associated with stromatolites and other microbialites around Australia at sites that have hardly or not at all been assessed before: Jenolan and Wombeyan Caves in NSW, Magnetic Island in QLD and alkaline and hypersaline lakes in SA and WA. I profiled the microbial communities in order to determine their relatedness. The effect of different environmental parameters on community composition was also investigated. By screening for non-ribosomal peptide synthesase (NRPS) and polyketide synthesase (PKS) genes, the potential of these communities to produce bioactive natural products was evaluated. Bringing environmental, natural product and community data together, I shed light on the dynamics of these specialized microbial assemblages and help in the discovery of potential new drugs derived from microorganisms.