Among the many ecosystem services provided by mangrove ecosystems, their role in carbon (C) sequestration and storage is quite high compared to other tropical forests. Mangrove forests occupy less than 1 % of tropical forested areas but account for approximately 3 % of global carbon sequestration by tropical forests. Yet there remain many areas where little data on the size and variation of mangrove C stocks exist. To address this gap and examine the range of C stocks in mangroves at landscape scales, we quantified C stocks of Honduran mangroves along the Pacific and Caribbean coasts and the Bay Islands. We also examined differences in ecosystem C stocks due to size and structure of mangrove vegetation found in Honduras. Ecosystem C stocks ranged from 570 Mg C ha-1 in the Pacific coast to ~1000 Mg C ha-1 in Caribbean coast and the Bay Islands. Ecosystem C stocks on the basis of mangrove structure were 1200, 800 and 900 Mg C ha-1, in low, medium and tall mangroves, respectively. We did not find significant differences in ecosystem C stocks on the basis of location (Pacific coast, Caribbean coast and Bay Islands) or mangrove type (low, medium and tall). Mangrove soils represented the single largest pool of total C in these ecosystems, with 87, 81 and 94 % at the Pacific coast, Caribbean coast and the Bay Islands, respectively. While there were no significant differences in total ecosystem stocks among mangrove types, there were differences in where carbon is stored. Mangrove soils among low, medium and tall mangroves contained 99, 93 and 80 % of the total ecosystem C stocks. In addition, we found a small yet significant negative correlation between vegetation C pools and pore water salinity and pH at the sampled sites. Conversion of mangroves into other land use types such as aquaculture or agriculture could result in loses of these soil C reserves due to mineralization and oxidation. Coupled with their other ecosystem services, an understanding of the size of mangrove ecosystem C stocks underscores their values in the formulation of conservation and climate change mitigation strategies in Central America.