Marine heatwaves (MHWs) significantly alter pelagic microbiology, as shown by a study analyzing data from thousands of Southern Hemisphere samples. During the 2015/16 Tasman Sea MHW, temperatures approached or exceeded the upper thermal limits of many endemic taxa, causing a shift in microbial assemblages to niche states aligned with sites over 1000 km equatorward. This shift was driven by higher temperatures and lower nutrient conditions associated with MHWs, leading to changes in microbial diversity and novel assemblage compositions. The most significant effects on microbial assemblages occurred during warmer months when temperatures exceeded climatological bounds. Trends across multiple MHWs suggest these changes are emergent properties of temperate ocean warming, which may aid in monitoring, prediction, and adaptation efforts. MHWs are prolonged ocean warming events that disrupt coastal ecosystems globally. They are linked to large-scale climate modes, with increasing frequency and intensity due to climate change. The frequency, intensity, and duration of MHWs have increased over the last century, linked to anthropogenic global warming, and are projected to continue. By the late 21st century, widespread near-permanent MHW status could become the "new-normal" in large oceanic regions. Reconstructed datasets suggest many parts of the ocean are already experiencing near-constant heat stress compared to conditions a century ago. Extreme MHW events have significant ecological and socioeconomic impacts, including mass mortality events in marine fauna and flora. These events can lead to impacts on commercially important fisheries and aquaculture systems or even total collapse. The loss of biodiversity, ecosystem function, and productivity from MHWs has economic costs, often exceeding billions of dollars. While the response of microbial assemblages remains understudied, temperature is a key trait determining microbial biogeography and assemblage composition. The study used a highly standardised molecular dataset to describe Southern Hemisphere marine microbial composition in thousands of samples linked to in situ oceanic conditions. The dataset included samples from latitudes 0–66°S, depths 0 m–~6000 m, and water temperatures -2–32°C in the Pacific, Indian, and Southern Oceans, as well as the Tasman, Coral, Arafura, and Timor Seas. The combined molecular and oceanographic dataset was used to generate indices describing the generalised niche characteristics or environmental preferences of microbial species and assemblages. The study found that during the 2015/16 MHW, bacterial and archaeal assemblages were under some degree of seasonal thermal stress, while eukaryote assemblages maintained a higher CTI and remained under positive thermal bias. The CTI ~ temperature relationship varied considerably when sampled over time at different locations. The study also found that during the 2015/16 MHW, the slope of the bacterial and archaeal CTIMarine heatwaves (MHWs) significantly alter pelagic microbiology, as shown by a study analyzing data from thousands of Southern Hemisphere samples. During the 2015/16 Tasman Sea MHW, temperatures approached or exceeded the upper thermal limits of many endemic taxa, causing a shift in microbial assemblages to niche states aligned with sites over 1000 km equatorward. This shift was driven by higher temperatures and lower nutrient conditions associated with MHWs, leading to changes in microbial diversity and novel assemblage compositions. The most significant effects on microbial assemblages occurred during warmer months when temperatures exceeded climatological bounds. Trends across multiple MHWs suggest these changes are emergent properties of temperate ocean warming, which may aid in monitoring, prediction, and adaptation efforts. MHWs are prolonged ocean warming events that disrupt coastal ecosystems globally. They are linked to large-scale climate modes, with increasing frequency and intensity due to climate change. The frequency, intensity, and duration of MHWs have increased over the last century, linked to anthropogenic global warming, and are projected to continue. By the late 21st century, widespread near-permanent MHW status could become the "new-normal" in large oceanic regions. Reconstructed datasets suggest many parts of the ocean are already experiencing near-constant heat stress compared to conditions a century ago. Extreme MHW events have significant ecological and socioeconomic impacts, including mass mortality events in marine fauna and flora. These events can lead to impacts on commercially important fisheries and aquaculture systems or even total collapse. The loss of biodiversity, ecosystem function, and productivity from MHWs has economic costs, often exceeding billions of dollars. While the response of microbial assemblages remains understudied, temperature is a key trait determining microbial biogeography and assemblage composition. The study used a highly standardised molecular dataset to describe Southern Hemisphere marine microbial composition in thousands of samples linked to in situ oceanic conditions. The dataset included samples from latitudes 0–66°S, depths 0 m–~6000 m, and water temperatures -2–32°C in the Pacific, Indian, and Southern Oceans, as well as the Tasman, Coral, Arafura, and Timor Seas. The combined molecular and oceanographic dataset was used to generate indices describing the generalised niche characteristics or environmental preferences of microbial species and assemblages. The study found that during the 2015/16 MHW, bacterial and archaeal assemblages were under some degree of seasonal thermal stress, while eukaryote assemblages maintained a higher CTI and remained under positive thermal bias. The CTI ~ temperature relationship varied considerably when sampled over time at different locations. The study also found that during the 2015/16 MHW, the slope of the bacterial and archaeal CTI