Elevated levels of tropical tropospheric ozone (O3) and carbon monoxide (CO) and decreased water (H2O) vapor were observed by the Tropospheric Emission Spectrometer (TES) in the region of Indonesia and the eastern Indian Ocean during the coincident positive phases of the El Niño Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) in late 2006. Using the chemical transport model GEOS-Chem, we show that the elevated CO results from increased biomass burning in Indonesia during the ENSO/IOD-induced drought and quantify the effect of the fires and other factors on O3. In the region of highest CO (˜200 ppb), the contribution of the fires to enhanced O3 is ˜45% in October, ˜75% in early November, and only 10% in December. More lightning in late 2006 compared to 2005 causes an increase in O3 of a few parts per billion. Dynamical changes increase O3 over a larger region than fire emissions which mainly increase O3 at 10°N-10°S in October and November. The model matches the O3 anomaly in October but underestimates it in November and December, which we ascribe to overly active convection in the model in late 2006, based on an analysis of outgoing longwave radiation (OLR) data. An underestimate of NOx emissions from soils may also contribute to the disparity at the end of the year. A dramatic decrease in O3 in late 2006 in equatorial Africa and the western Indian Ocean is reproduced by the model and is caused by highly enhanced convection in 2006, likely associated with the IOD.