Mangrove forests offer important ecosystem services, including their high capacity for carbon sequestration and stocking. However, they face rapid degradation and loss of ecological resilience particularly at local scales due to human pressure. We conducted inventory of mangrove forests to characterise forest stand structure and estimate carbon stocks in the small estuarine mangroves of Geza and Mtimbwani in Tanga, Tanzania. Forest structure, above-ground carbon (AGC), and below-ground carbon (BGC) were characterised. Soil carbon was estimated to 1 m depth using loss on ignition procedure. Six common mangrove species were identified dominated by Avicennia marina (Forsk.) Vierh. and Rhizophora mucronata Lamarck. Forest stand density and basal area were 1740 stems ha−1 and 17.2 m2 ha−1 for Geza and 2334 stems ha−1 and 30.3 m2 ha−1 for Mtimbwani. Total ecosystem carbon stocks were 414.6 Mg C ha−1 for Geza and 684.9 Mg C ha−1 for Mtimbwani. Soil carbon contributed over 65% of these stocks, decreasing with depth. Mid zones of the mangrove stands had highest carbon stocks. These data demonstrate that studied mangroves are potential for carbon projects and provide the baseline for monitoring, reporting, and verification (MRV) to support the projects.This work was funded by a research grant from the Bilateral Marine Science Programme supported by Sida through the Institute of Marine Sciences of the University of Dar es Salaam.