The carbon cycle includes important fluxes of methane (CH4) and carbon dioxide (CO2) between the ecosystem and the atmosphere. The fluxes may acquire either positive (release) or negative values (consumption). We calculated these fluxes based on short-campaign in situ chamber measurements from four ecosystems of South Vietnam: intact mountain rain forest, rice field, Melaleuca forest and mangroves (different sites with Avicennia or Rhizophora and a typhoon-disturbed gap). Soil measurements were supplemented by chamber measurements of gas fluxes from the tree stems. Measuring CH4 and CO2 together facilitates the assessment of the ratio between these two gases in connection with current conditions and specificity of individual ecosystems. The highest fluxes of CH4 were recorded in the Melaleuca forest, being within the range from 356.7 to 784.2 mg CH4–C m−2 day−1 accompanied by higher fluxes of CH4 release from Melaleuca tree stems (8.0–262.1 mg CH4–C m−2 day−1). Significant negative soil fluxes of CH4 were recorded in the mountain rain forest, within the range from − 0.3 to − 0.8 mg CH4–C m−2 day−1. Fluxes of CO2 indicate prevailing aerobic activity in the soils of the ecosystems investigated. Quite a large variability of CO2 fluxes was recorded in the soil of the Avicennia mangroves. The in situ measurements of different ecosystems are fundamental for follow-up measurements at different levels such as aerial and satellite gas fluxes observations.