Bioregional categorisation of the Australian marine environment is essential to conserve and manage entire ecosystems, including the biota and associated habitats. It is important that these regions are optimally positioned to effectively plan for the protection of distinct assemblages. Recent climatic variation and changes to the marine environment in Southwest Australia (SWA) have resulted in shifts in species ranges and changes to the composition of marine assemblages. The goal of this study was to determine if the current bioregionalisation of SWA accurately represents the present distribution of shallow-water reef fishes across 2000 km of its subtropical and temperate coastline. Data was collected in 2015 using diver-operated underwater stereo-video surveys from 7 regions between Port Gregory (north of Geraldton) to the east of Esperance. This study indicated that (1) the shallow-water reef fish of SWA formed 4 distinct assemblages along the coast: one Midwestern, one Central and 2 Southern Assemblages; (2) differences between these fish assemblages were primarily driven by sea surface temperature, Ecklonia radiata cover, non-E. radiata (canopy) cover, understorey algae cover, reef type and reef height; and (3) each of the 4 assemblages were characterised by a high number of short-range Australian and Western Australian endemic species. The findings from this study suggest that 4, rather than the existing 3 bioregions would more effectively capture the shallow-water reef fish assemblage patterns, with boundaries having shifted southwards likely associated with ocean warming.