Gabonese’s estuary is an important coastal mangrove setting and soil plays a key role in mangrove carbon storage in mangrove forests. However, the spatial variation in soil organic carbon (SOC) storage remain unclear. To address this gap, determining the SOC spatial variation in Gabonese’s estuarine is essential for better understanding the global carbon cycle. The present study compared soil organic carbon between northern and southern sites in different mangrove forest, Rhizophora racemosa and Avicennia germinans. The results showed that the mean SOC stocks at 1 m depth were 256.28 ± 127.29 MgC ha−1. Among the different regions, SOC in northern zone was significantly (p < 0.001) higher (232.45 ± 120.81 MgC ha−1) than that in the southern zone (143.19 ± 44 MgC ha−1). At all sites, SOC stocks were significantly higher in Rhizophora racemose (192.2 ± 114.17 MgC ha−1) than in Avicenia germinans (130.12 ± 161.16 MgC ha−1) (p < 0.001). The deeper layers contained higher SOC stocks (254.62 ± 128.09 MgC ha−1) than upper layers (55.42 ± 25.37 MgC ha−1). The study highlights that low deforestation rate have led to less CO2 (705.3 Mg CO2e ha−1 - 922.62 Mg CO2e ha−1) emissions than most sediment carbon-rich mangroves in the world. These results highlight the influence of soil texture and mangrove forest types on the mangrove SOC stocks. The first national comparison of soil organic carbon stocks between mangroves and upland tropical forests indicated SOC stocks were two times more in mangroves soils (51.21 ± 45.00 MgC ha−1) than primary (20.33 ± 12.7 MgC ha−1), savanna and cropland (21.71 ± 15.10 MgC ha−1). We find that mangroves in this study emit
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