This study investigates the bacterial communities (microbiome) of damselfishes collected in the Great Barrier Reef. Wild damselfish representing 10 species (Abudefduf sexfasciatus , Abudefduf whitleyi , Acanthochromis polyacanthus , Chromis atripectoralis , Pomacentrus moluccensis , Dischistodus perspicillatus , Dischistodus pseudochrysopoecilus , Pomacentrus wardi , Stegastes apicalis , Stegastes nigricans ) were collected from Heron Island. These species represent two feeding guilds planktivorous and algae-farmers. Microbiome samples from the stomach, anterior intestine, mid-intestine and posterior intestines weer collected from three individuals of each of the 10 species. V1-V3 regions of the 16S rRNA gene were sequenced to understand the differences in intestinal microbiomes between the 10 damselfish species, the two feeding guilds and the intestinal regions. The second component of this study was an experimental investigation into the effects of heat stress on damselfish microbiomes.