Abstract. In order to improve our understanding of air quality in Southeast Asia, the anthropogenic emissions inventory must be well represented. In this work, we apply different anthropogenic emission inventories in the Weather Research and Forecasting Model with Chemistry (WRF-Chem) version 3.3 using MOZART gas-phase chemistry and GOCART aerosols to examine the differences in predicted carbon monoxide (CO) and ozone (O3) surface mixing ratios for Southeast Asia in March and December 2008. The anthropogenic emission inventories include the Reanalysis of the TROpospheric chemical composition (RETRO), the Intercontinental Chemical Transport Experiment-Phase B (INTEX-B), the MACCity emissions (adapted from the Monitoring Atmospheric Composition and Climate and megacity Zoom for the Environment projects), the Southeast Asia Composition, Cloud, Climate Coupling Regional Study (SEAC4RS) emissions, and a combination of MACCity and SEAC4RS emissions. Biomass burning emissions are from the Fire Inventory from NCAR (FINNv1) model. WRF-chem reasonably predicts the 2 m temperature, 10 m wind, and precipitation. In general, surface CO is underpredicted by WRF-Chem while surface O3 is overpredicted. The NO2 tropospheric column predicted by WRF-Chem has the same magnitude as observations, but tends to underpredict NO2 column over the equatorial ocean and near Indonesia. Simulations using different anthropogenic emissions produce only a slight variability of O3 and CO mixing ratios, while biomass burning emissions add more variability. The different anthropogenic emissions differ by up to 20% in CO emissions, but O3 and CO mixing ratios differ by ~4.5% and ~8%, respectively, among the simulations. Biomass burning emissions create a substantial increase for both O3 and CO by ~29% and ~16%, respectively, when comparing the March biomass burning period to December with low biomass burning emissions. The simulations show that none of the anthropogenic emission inventories are better than the others and any of the examined inventories can be used for air quality simulations in Southeast Asia.