Shifts in microbial communities represent a fast response mechanism for organisms to respond to environmental conditions and are likely to be essential in assisting the acclimatization of host species to the increased temperatures associated with climate change. The Persian/Arabian Gulf is the world’s warmest sea and therefore may serve as an informative model for predicting how the microbiome will change under climate change conditions. In this study, we investigated temporal and geographic changes in the diversity, stability, and composition of the sea urchin gut microbiome with the aim to identify the main drivers of microbial community variation and identify microbial taxa that are predictive of thermal environment. We generated two independent datasets, the first of which consisted of sampling six different reef sites from the Persian/Arabian Gulf and the Gulf of Oman in both summer and winter. The second dataset sampled one site within the Persian/Arabian Gulf at eight different time points across one year to investigate seasonal microbiome fluctuations. The results show that the gut microbiome is different across thermally variable habitats, displays temporal shifts that correlate with temperature change, and is impacted by temperature through measures of community dispersion. Importantly, the temperature correlation analysis of the two datasets highlighted taxonomic redundancy and in some cases, the exact same microbes, which may point to biomarkers of temperature increases. These results are informative for our understanding of how the environment drives microbial diversity as well as elucidating microbial taxa that may play a key role during thermal stress resilience.