Globally, changes in the geographical distribution of species as a result of climate change are becoming frequently documented occurrences. In Western Australia, several tropical herbivorous fish species, including the rabbitfish Siganus fuscescens, have recently expanded their southern boundary range. Microbial communities both impact and are impacted by the host organism, and are therefore a reflection of the host’s health. The new species range provides colder temperatures and new food resources to exploit, presenting a unique opportunity to assess the factors that shape spatial variability of gastrointestinal microbes inhabiting these fish. S. fuscescens hosted distinct communities of microbes among four populations. However, these differences were not related to latitudinal gradient indicating that local factors such as diet may have a strong impact on shaping the microbial communities. The midgut and hindgut microbial communities were also significantly different from one another and from the local sea water microbial communities which indicated these communities have formed specialised associations within S. fuscescens. Short chain fatty acids were measured within the hindgut, with relatively similar amounts found among sites. These results indicate that the microbial communities of range shifting S. fuscescens are highly active and have adapted within fish from the new southern locations.