Background: The dry transitional forests of the southern Amazonia have received little attention from a carbon cycling and ecosystem function perspective, yet they represent ecosystems that may be impacted by global climate change in the future. Aims: To compare the full carbon cycle for two 1-ha forest plots that straddle the ecotone between humid forest and dry forest in Amazonia, ca. 100 km from Santa Cruz, Bolivia. Methods: 2.5 years of measurements of the components of net primary production (NPP) and autotrophic respiration were collected. Results: Total NPP was 15.5 ± 0.89 Mg C ha-1 year-1 at the humid site and 11.27 ± 0.68 Mg C ha-1 year-1 at the dry site; a total Gross Primary Production (GPP) of 34.14 ± 2.92 Mg C ha-1 year-1 and 26.88 ± 2.70 Mg C ha-1 year-1 at the two sites. Carbon use efficiency for both sites was higher than reported for other Amazonian forests (0.45 ± 0.05 and 0.42 ± 0.05). Conclusions: Drier soil conditions selected for the dry deciduous tree species which had higher leaf photosynthesis and total GPP. NPP allocation patterns were similar at the two sites, suggesting that in terms of carbon allocation, the dry forests of the southern Amazonia behave as a scaled-down version of wetter humid forests. © 2014 Copyright 2013 Botanical Society of Scotland and Taylor & Francis.