The source and sinks of carbon dioxide (CO2) and methane (CH4) due to anthropogenic and natural biospheric activities were estimated for the South Asian region (Bangladesh, Bhutan, India, Nepal, Pakistan and Sri Lanka). Flux estimates were based on top-down methods that use inversions of atmospheric data, and bottom-up methods that use field observations, satellite data, and terrestrial ecosystem models. Based on atmospheric CO2 inversions, the net biospheric CO2 flux in South Asia (equivalent to the Net Biome Productivity, NBP) was a sink, estimated at −104 ± 150 Tg C yr−1 during 2007–2008. Based on the bottom-up approach, the net biospheric CO2 flux is estimated to be −191 ± 193 Tg C yr−1 during the period of 2000–2009. This last net flux results from the following flux components: (1) the Net Ecosystem Productivity, NEP (net primary production minus heterotrophic respiration) of −220 ± 186 Tg C yr−1 (2) the annual net carbon flux from land-use change of −14 ± 50 Tg C yr−1, which resulted from a sink of −16 Tg C yr−1 due to the establishment of tree plantations and wood harvest, and a source of 2 Tg C yr−1 due to the expansion of croplands; (3) the riverine export flux from terrestrial ecosystems to the coastal oceans of +42.9 Tg C yr−1; and (4) the net CO2 emission due to biomass burning of +44.1 ± 13.7 Tg C yr−1. Including the emissions from the combustion of fossil fuels of 444 Tg C yr−1 for the 2000s, we estimate a net CO2 land–atmosphere flux of 297 Tg C yr−1. In addition to CO2, a fraction of the sequestered carbon in terrestrial ecosystems is released to the atmosphere as CH4. Based on bottom-up and top-down estimates, and chemistry-transport modeling, we estimate that 37 ± 3.7 Tg C yr−1 were released to atmosphere from South Asia during the 2000s. Taking all CO2 and CH4 fluxes together, our best estimate of the net land–atmosphere CO2-equivalent flux is a net source of 334 Tg C yr−1 for the South Asian region during the 2000s. If CH4 emissions are weighted by radiative forcing of molecular CH4, the total CO2-equivalent flux increases to 1148 Tg C yr−1 suggesting there is great potential of reducing CH4 emissions for stabilizing greenhouse gases concentrations.