Measurements of the organic carbon inventory, its stable isotopic composition and radiocarbon content were used to deduce vegetation history from two soil profiles in arboreal and grassy savanna ecotones in the Brazilian Pantanal. The Pantanal is a large floodplain area with grass-dominated lowlands subject to seasonal flooding, and arboreal savanna uplands which are only rarely flooded. Organic carbon inventories were lower in the grassy savanna site than in the upland arboreal savanna site, with carbon decreasing exponentially with depth from the surface in both profiles. Changes in 13C of soil organic matter (SOM) with depth differed markedly between the two sites. Differences in surface SOM 13C values reflect the change from C3 to C4 plants between the sites, as confirmed by measurements of 13C of vegetation and the soil surface along a transect between the upland closed-canopy forest and lowland grassy savanna. Changes of 13C in SOM with depth at both sites are larger than the 3–4 per mil increases expected from fractionation associated with organic matter decomposition. We interpret these as recording past changes in the relative abundance of C3 and C4 plants at these sites. Mass balances with 14C and 13C suggest that past vegetational changes from C3 to C4 plants in the grassy savanna, and in the deeper part of the arboreal savanna, occurred between 4600 and 11 400 BP, when major climatic changes were also observed in several places of the South American Continent. The change from C4 to C3, observed only in the upper part of the arboreal savanna, was much more recent (1400 BP), and was probably caused by a local change in the flooding regime.