During the SHIVA (Stratospheric Ozone: Halogen Impacts in a Varying Atmosphere) campaign in Nov. and Dec. 2011 a number of polluted air masses were observed in the marine and terrestrial boundary layer (0 – 2 km) and in the free troposphere (2 – 12 km) over Borneo/Malaysia. The measurements include isoprene, CO, CO2, CH4, N2O, NO2, SO2 as primary pollutants, O3 and HCHO as secondary pollutants, and meteorological parameters. This set of trace gases can be used to fingerprint different sources of local and regional air pollution (e.g., biomass burning and fossil fuel burning, gas flaring on oil rigs, emission of ships and from urban areas, volcanic emissions, and biogenic emissions). Individual sources and location can be identified when the measurements are combined with a nested-grid regional scale chemical and meteorological model and lagrangian particle dispersion model (e.g., CCATT-BRAMS and FLEXPART). In the case of the former, emission inventories of the primary pollutants provide the basis for the trace gas simulations. In this region, the anthropogenic influence on air pollution seems to dominate over natural causes. For example, CO2 and CH4 often show strong correlations with CO, suggesting biomass burning or urban fossil fuel combustion dominates the combustion sources. The study of the CO/CO2 and CH4/CO ratios can help separate anthropogenic combustion from biomass burning pollution sources. In addition, these ratios can be used as a measure of combustion efficiency to help place the type of biomass burning particular to this region within the wider context of fire types found globally. On several occasions, CH4 enhancements are observed near the ocean surface, which are not directly correlated with CO enhancements thus indicating a non-combustion-related CH4 source. Positive correlations between SO2 and CO show the anthropogenic influence of oil rigs located in the South China Sea. Furthermore, SO2 enhancements are observed without any increase in CO, indicating possible volcanic emissions from the Indonesian islands to the South and East and the Philippines to the North East. The regional pollution seems to be influenced by emissions from Singapore, Philippines, Indonesia and Peninsula Malaysia, and on occasion by anthropogenic emissions from Thailand, Vietnam, Australia, and China.