Global inventories that show mangrove forests have rich carbon stores currently lack data from arid areas where carbon stocks may be functionally impoverished relative to humid regions. We quantified total carbon stocks (C) of three arid Avicennia marina stands in Qatar and report an aboveground biomass allometric equation and the first below ground biomass allometric equation in the region. The allometric relationships indicate that below ground mangrove C stocks in arid locations are more important than previously reported. Comparison of previously published and our locally developed allometric equations show that A. marina in Qatar allocate comparatively more biomass to below ground components than the same species in tropical humid settings, which is consistent with plant adaptations to living in stressed conditions. Total C stocks were 45.70 ± 3.70 Mg C ha−1, of which tree and soil C stocks to 50 cm depth represented 10.18 ± 0.82 Mg C ha−1 and 35.52 ± 2.88 Mg ha−1 respectively. Soil C stocks to 1 m depth were 50.17 ± 6.27 Mg C ha−1. Overall, mangroves sustain relatively small C stocks in the arid, hypersaline environment of Qatar, which may be due to both relatively low tree productivity and growth, as well as limited rainfall-driven transport of terrigenous sediment inputs. By providing further estimates of mangrove carbon at their climatic extremes, these results can contribute to a better quantification of global mangrove carbon, reduce uncertainty in below ground tree C estimates from arid mangroves and have implications for mangrove carbon stocks in the face of climate change.