The vulnerability of coral reefs to environmental stress has traditionally been assessed by determining how key species respond to particular environmental factors. Over the past decade however, molecular science has revealed the critical importance of microorganisms to invertebrate health, fitness and ultimately survival (Figs. 1 and 2). Therefore, if we are to understand and predict the sensitivity and vulnerability of reef organisms we need to assess the stress response in both the host and its associated microbiome (holobiont). Research within this program applies metagenomic and transcriptomic tools to delivers stakeholders with knowledge of how temperature, ocean acidification, nutrient enrichment and increased sedimentation influence the functional roles of marine microbial symbionts within their hosts. In this research program we also move beyond measuring specific thresholds and attempt to forecast the long term consequences of climate change and environmental stress for invertebrate populations.