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Mangrove forests along the coastlines of the tropical and sub-tropical western Atlantic are intermittently impacted by hurricanes and can be damaged by high-speed winds, high-energy storm surges, and storm surge sediment deposits that suffocate tree roots. This study quantified trends in damage, delayed mortality, and early signs of below- and aboveground recovery in mangrove forests in the Lower Florida Keys and Ten Thousand Islands following direct hits by Hurricane Irma in September 2017. Mangrove trees suffered 19% mortality at sites in the Lower Florida Keys and 11% in the Ten Thousand Islands 2–3 months post-storm; 9 months post-storm, mortality in these locations increased to 36% and 20%, respectively. Delayed mortality of mangrove trees was associated with the presence of a carbonate mud storm surge deposit on the forest floor. Mortality and severe branch damage were more common for mangrove trees than for mangrove saplings. Canopy coverage increased from 40% cover 1–2 months post-storm to 60% cover 3–6 months post-storm. Canopy coverage remained the same 9 months post-storm, providing light to an understory of predominantly Rhizophora mangle (red mangrove) seedlings. Soil shear strength was higher in the Lower Florida Keys and varied with depth; no significant trends were found in shear strength between fringe or basin plots. Rates of root growth, as assessed using root in-growth bags, were relatively low at 0.01–11.0 g m−2 month−1 and were higher in the Ten Thousand Islands. This study demonstrated that significant delayed mangrove mortality can occur 3–9 months after a hurricane has passed, with some mortality attributable to smothering by storm surge deposits.