Future increases in oceanic temperature are predicted to occur globally. In general, environmental change will probably have strong impacts on native microbial communities and these impacts are likely to be complex, species-specific and difficult to predict. With respect to studying the effects of temperature on benthic marine habitats, the Western Australian coastline presents a unique opportunity: it is one of the last remaining areas of relatively pristine marine habitats in the world and has a well-defined temperature gradient due to the Leeuwin Current. Here, we examined in situ effects of temperature using a space for time sampling design along hundreds of kilometres of the WA coastline. Our analyses include microbiomes from a range of key marine organisms including a coralline alga, a sponge, a coral and an herbivorous fish. In all organisms there were strong beta diversity shifts among locations along the WA coastline. However, in general there were no substantial changes in alpha diversity between locations nor was alpha diversity high in locations at the edge of species ranges as may be expected under dysbiosis of host associated communities.