GHG Emission in term of methane and nitrous oxide were estimated using IPCC method with specific emission factor derived from the experimental site in Thailand. The estimation covered rain fed and irrigation rice fields both first and second cultivation in a year and the typical forest types in Thailand and Cambodia. GIS emission map of two land use were established for Mekong River Basin Sub-region using the information from each country. Identification of high emission and sensitive area are at the northeast region of Thailand and around TonleSap area in Cambodia. Carbon monoxide and particulate matter from rice field residue burning and forest fire were also estimated using method developed from IPCC. Data from remote sensing was used to compare the result of GIS map established from the studies. Hot spot of forest fire and biomass burning in Mekong River Basin Sub-region were identified. Both forest fires and paddy field burning activities are observed to peak during the first and last few months of the year from January to April and October to December. This seasonality pattern corresponds to the dry season, period during which there is a lack of rainfall and vegetation fires are therefore detected to take place. Considering biomass burning and biogenic GHG emission, forests in GMS are sources of CO and TPM from biomass burning as well as less significant amount of N2O from forest soil but are the sink of methane form forest soil. Rice fields with the high contribution for methane emission are likely to emphasize in terms of CO and TPM for local emission problems, while emission from forest should be concerned for the regional or trans-boundary problems.