A growing body of evidence indicates that temperate marine ecosystems are being tropicalised due to the poleward extension of tropical species. Such climate mediated changes in species distribution patterns have the potential to profoundly alter temperate communities, as this advance can serve to push temperate taxa, many of which are southern Australian endemics, southward. These changes can lead to cascading effects for the biodiversity and function of coastal ecosystems, including contraction of ranges/habitats of sensitive cool water species. Hence there is growing concern for the future of Australia’s temperate marine biodiversity. Here we examine the diversity and abundance of marine flora and fauna at two reefs near Perth’s metropolitan area—Minden Reef and Roe Reef. We report the presence of 427 species of marine flora and fauna from eight taxon groups occurring in the Perth metropolitan area; at least three species of which appear to be new to science. Our data also extends the known range of 15 species, and in numerous instances, thousands of kilometres south from the Kimberley or Pilbara and verifies that tropicalisation of reef communities in the Perth metropolitan area is occurring. We report the presence of 24 species endemic to south-west Australia that may be at risk of range contractions with continued ocean warming. The results of these surveys add to our knowledge of local nearshore marine environments in the Perth metropolitan area and support the growing body of evidence that indicates a diverse and regionally significant marine fauna occurs in temperate Western Australia. Regular, repeated survey work across seasons is important in order to thoroughly document the status of marine biodiversity in this significant transition zone.