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Extreme events have profound ecological impacts on species and ecosystems, including range contractions and collapse of entire ecosystems. Although theory predicts that extreme events cause loss of genetic diversity, empirical demonstrations are rare, obscuring implications for future adaptive capacity of species and populations. Here, we use rare genetic data from before an extreme event to empirically demonstrate massive and cryptic loss of genetic diversity across ∼800 km of underwater forests following the most severe marine heatwave on record. Two forest-forming seaweeds (Sargassum fallax and Scytothalia dorycarpa) lost ∼30%–65% of average genetic diversity within the 800-km footprint of the heatwave and up to 100% of diversity at some sites. Populations became dominated by single haplotypes that were often not dominant or present prior to the heatwave. Strikingly, these impacts were cryptic …