Globally, marine species distributions are being modified as a result of rising sea surface temperature. On the west coast of Australia, the southern distributional limits of several tropical herbivorous fish species, including the rabbitfish Siganus fuscescens, have recently expanded into temperate regions. Microbes are fundamentally important to animal health, demanding an understanding of their variation in studies of animal adaption. Range-shifting S. fuscescens thus provide a unique opportunity to assess the stability of gastrointestinal microbes under varying environmental conditions. Here, the gastrointestinal microbial communities of S. fuscescens were characterised over 2000km of Western Australia’s coastline, including in the species’ historical and current southern range limit. MiSeq Illumina sequencing of the 16S rRNA gene demonstrated that the microbial community differed among populations, and there was a general decrease in hindgut microbial community similarity with distance. However, the population in the newly expanded range had similar hindgut microbial communities to one population in the historical range and levels of short chain fatty acids, an indicator of microbial fermentation activity, were similar among tropical and temperate locations. These data suggest that flexibility in the hindgut microbiome may play a role in enabling range-shifting herbivores to colonise new habitats.