Ucides cordatus is a semi-terrestrial crab and key species endemic to mangrove areas of eastern Americas. In North-eastern Brazil this crab holds a major socio-economic function for artisanal fisheries, as in the São Francisco River Estuary (10°30′27″S 36°23′45″W). Nevertheless, decreases in this species’ stock have been reported since 2000, requiring assessments of the crab population for conservation and management purposes. This study aims at assessing the population status and the fishery potential of this species in the mangroves of this estuary and suggests strategies for its fishery and conservation, according to the guidelines of the National Management Plan for U. cordatus Sustainable Use. Six different sites established in 30 km2 of mangroves were sampled, with the density of U. cordatus burrows estimated to evaluate the population structure using the measure of burrow diameters. Results show that the crab mean burrow size was 56.82 (±12.2) mm and that the medium-size crabs (40–70 mm) are the most abundant. The total mean crab density was 1.2 crabs m−2, from which the density of crabs in commercial size (0.85 ± 0.55 crabs m−2) was significantly higher than those in non-commercial size (0.35 ± 0.21 burrow m−2). These mangroves showed a high potential for the crab fishery, with an immediate extractive potential (IEP) of 71.2% and future extractive potential (FEP) of 28.8%. Nevertheless, a lower crab density, probably due to high crab mortality, mangrove deforestation for shrimp farming and high fishery pressure, is a limiting factor for local fishery. We conclude that mangrove areas more appropriate for U. cordatus fishery (extractive areas) show higher mean crab size, IEP and density of commercial crabs, wherein a fixed exploitation rate or/and a fixed escapement rule should be considered. Exclusion areas, intended for the conservation, show lower values of these population parameters and higher FEP, wherein the fishery should be prohibited. These management strategies should also be considered in other Brazilian mangrove areas showing similar crab population structure, thus contributing to the National Management Plan for U. cordatus Sustainable Use.