Hurricanes Irma and Maria ravaged the mangroves of St. John, U.S. Virgin Islands, in 2017. Basal area losses were large (63–100%) and storm losses of carbon associated with aboveground biomass amounted to 11.9–43.5 Mg C/ha. Carbon biomass of dead standing trees increased 8.1–18.3 Mg C/ha among sites, and carbon in coarse woody debris on the forest floor increased 1.9–18.2 Mg C/ha, with effects varying by mangrove typology. While St. John has only ~45 ha of mangroves, they exist as isolated basins, salt ponds, and fringe mangroves; the latter sometimes support diverse marine communities. Salt pond and fringe mangroves had proportionately more organic carbon (46.3 Mg C/ha) than inorganic carbon (1.1 Mg C/ha) in soils than isolated basins. Soil organic carbon was also appreciable in isolated basins (30.8 Mg C/ha) but was matched by inorganic C (36.7 Mg C/ha), possibly due to adjacent land use history (e.g., road construction), previous storm overwash, or geomorphology. Soil nitrogen stocks were low across all typologies. Mangroves had limited regeneration 26 months after the storms, and recovery on St. John may be hindered by pre-storm hydrologic change in some stands, and potential genetic bottlenecks and lack of propagule sources for expedient recovery in all stands.