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Threatened globally, mangrove forests provide many ecosystem services, including blue carbon storage. These forests, and the services that they provide, are distributed across spatio-temporally variable coastal landscapes and a range of environmental conditions, though this variability is underappreciated in the blue carbon literature. The Galapagos, Ecuador, presents the opportunity to explore spatial variability in carbon storage. This volcanically active archipelago features rocky shores and arid conditions at low elevations (< 500 mm/year), with patchy forests under far from optimal conditions. At 29 mangrove sites, we cored from the sediment surface down to basement rock, and samples were dried, weighed, and analyzed for their carbon content by GC-MS. Belowground carbon stocks range from < 50 Mg/ha to > 500 Mg/ha, i.e. from practically no carbon to values typical of lush, productive mangroves. This variability is driven principally by variation in sediment depth, with high inter-site variance associated with underlying lava substrate. The first to measure mangrove blue carbon in the Galapagos, this study reveals the spatial heterogeneity of the islands’ patchy mangroves. These results underscore the importance of local ecosystem constraints and natural variability in ecosystem service valuation for conservation prioritization.