Fish are the most speciose group of vertebrates and represent a fundamental resource with approximately 40% of the human population relying on wild caught or aquaculture fish as a principal source of protein. Fish are also critical components of reef systems, playing fundamental roles in nutrient cycling. Current understanding of the importance of fish-associated microbial communities is emerging, with most fish-microbiome research focussed on aquaculture species. Using examples of wild marine fish from the west coast Australia to the tropical islands of Japan, this research showcases ecological and evolutionary patterns in fish gut microbial communities. Key results indicate that range-expanding species maintain relatively robust gut microbial communities despite substantial shifts in diet availability; that fish gut microbiomes reflect levels of anthropogenic impact, in both tropical and temperate reef systems; and that the gut microbiome may serve as an early “biological” indicator of speciation via hybridization. Taken together, this body of work demonstrates the sensitivity of fish gut microbial communities and their utility as markers of host condition and rapid evolutionary change.