Coastal wetlands are among the most productive ecosystems and store large amounts of organic carbon (C) - the so termed "blue carbon". However, wetlands in the tropics and subtropics have been invaded by smooth cordgrass (Spartina alterniflora) affecting storage of blue C. To understand how S. alterniflora affects SOC stocks, sources, stability, and their spatial distribution, we sampled soils along a 2500 km coastal transect encompassing tropical to subtropical climate zones. This included 216 samplings within three coastal wetland types: a marsh (Phragmites australis) and two mangroves (Kandelia candel and Avicennia marina). Using δ13 C, C: nitrogen (N) ratios and lignin biomarker composition we traced changes in the sources, stability and storage of SOC in response to S. alterniflora invasion. The contribution of S. alterniflora-derived C up to 40 cm accounts for 5.6%, 23% and 12% in the P. australis, K. candel and A. marina communities, respectively, with a corresponding change in SOC storage of +3.5, -14 and -3.9 t C ha-1 . SOC storage did not follow the trend in aboveground biomass from the native to invasive species, or with vegetation types and invasion duration (7-15 years). SOC storage decreased with increasing mean annual precipitation (1000-1900 mm) and temperature (15.3-23.4 ℃). Edaphic variables in P. australis marshes remained stable after S. alterniflora invasion and so, their effects on SOC content were absent. In mangrove wetlands, however, electrical conductivity, total N and phosphorus, pH and active silicon were the main factors controlling SOC stocks. Mangrove wetlands were most strongly impacted by S. alterniflora invasion and efforts are needed to focus on restoring native vegetation. By understanding the mechanisms and consequences of invasion by S. alterniflora, changes in blue C sequestration can be predicted to optimize storage can be developed.