Microorganisms play critical roles in mediating reef health and stability via their ubiquitous involvement in nutrient cycling and interactions with reef macroorganisms, which can both promote reef health (e.g. microbial coral settlement cues) or destabilise it (viral infection/disease). However, publicly available microbial genomic reference data from coral reefs worldwide is limited, with previous large genomic surveys focussing instead on pelagic microbes (e.g. Tara Oceans). As Australia is home to the largest reef ecosystem in the world, there is unique opportunity to construct substantial genomic resources representing coral reef microorganisms. To address this, the Integrated Marine Observing System’s Marine Microbiome Initiative (IMOS-MMI) has collected samples from 48 sites spanning a full north-to-south transect of the Great Barrier Reef (GBR). Long read (nanopore) sequencing of these sites has generated >5,000 bacterial and archaeal genomes, with ~1400 being near-complete and several hundred fully circular, including dominant taxa like Pelagibacter that are typically not recovered with short-read sequencing. In addition, >100,000 putative viruses and >20,000 plasmids were recovered that can be linked to their hosts to assess their population dynamics, as well as multiple picoeukaryote genomes. The IMOS-MMI Database represents an unprecedented resource for studying the biology of the GBR and coral reefs globally.