Stromatolites are one of the most prevalent and recognizable components of the fossil record, dating back more than 3.7 Ga years. These structures are formed by the sediment trapping, binding and/or carbonate precipitating activities of microorganisms in response to their local environment. These long-lived ecosystems have had a profound impact on the habitability of the planet, as they are attributed to changing the global redox conditions via oxygenic photosynthesis, making modern stromatolites ideal model systems for investigating the underlying processes associated with the precipitation and dissolution of calcium carbonate. In this study, we compared the metagenomes (genetic material) of the three dominant stromatolite-forming microbial mat types against a non-stromatolite forming microbial mat from the hypersaline waters of Hamelin Pool, Shark Bay located in Western Australia – the largest, most expansive marine ecosystem in the world in which millions of stromatolites grow today. Investigational efforts focused on the particular members of the stromatolite forming microbial community as well as the genetic profile of the different mat types in an effort to elucidate a metagenomic ‘signature’ for the stromatolite forming mats as opposed to the non-stromatolite forming mat types.