Disease is emerging as an important impact of global climate change, due to the effects of environmental change on host organisms and their pathogens. Climate-mediated disease can have severe consequences in natural systems, particularly when ecosystem engineers, such as habitat-formers or top predators are affected, as any impacts can cascade throughout entire food webs. In temperate marine ecosystems, seaweeds are the dominant habitat-formers on rocky reefs. We investigated a putative bleaching disease affecting Delisea pulchra, a chemically defended seaweed that occurs within a global warming ‘hot-spot’ and assessed how patterns of this phenomenon were influenced by ocean temperature, solar radiation, algal chemical defences and microbial pathogens. Warmer waters were consistently and positively correlated with higher frequencies of bleaching in seaweed populations, but patterns of bleaching were not consistently influenced by light levels. Bleached thalli had low levels of antibacterial chemical defences relative to healthy conspecifics and this was observed across entire thalli of partially bleached algae. Microbial communities associated with bleached algae were distinct from those on the surfaces of healthy seaweeds. Direct testing of the importance of algal chemical defences, done here for the first time in the field, demonstrated that they protected the seaweed from bleaching. Treatment of algal thalli with antibiotics reduced the severity of bleaching in experimental algae, especially at high water temperatures. These results indicate that bleaching in D. pulchra is the result of temperature-mediated bacterial infections and highlight the potential for warming to influence disease dynamics by stressing hosts. Understanding the complex ways in which global change may affect important organisms such as habitat-forming seaweeds, is essential for the management and conservation of natural resources.