Recent studies have identified novel aquatic plant communities with a high level of endemism in ephemeral sandstone rock pools in the Northern Kimberley, one of the last botanical frontiers in Australia. An intrinsic link is apparent between the flora of these rock pools and their microbial communities, with biogenic ethylene produced by bacteria and fungi in response to wetting events regulating the timing and scale of seedling emergence events from the sediment seed bank. In this project, high throughput sequencing was used to characterise the fungal, algal and bacterial communities present in the rock pools and identify species which may be acting as drivers of floristic community composition. Sediment was examined from 98 rock pools across six sites. Forty samples of microbial crusts were also collected from the sandstone pavement adjacent to the rock pools. More than 1200 operational taxonomic units of fungi, algae (chlorophyta) and bacteria were found across all samples examined. The rock pools and crusts had distinctly different microbial communities and correlations were found between microbial community composition and a range of site factors. Potential links between specific groups of microbes and floristic communities are discussed.