A photochemical mechanism is a very important component of an air quality model, which simulates the change of pollutant concentrations due to chemical reactions in the air. The accuracy of model prediction is directly impacted by the photochemical mechanism. In this study, two state-of-the-science photochemical mechanisms, SAPRC07 and Master Chemical Mechanism (MCM) v3.1, were implemented in the Community Multi-scale Air Quality Model (CMAQ) version 4.6 developed by the US EPA to study a high ozone (O3) episode during the 2000 Texas Air Quality Study (TexAQS) from August 16, 2000 to September 7, 2000. Predicted O3 concentrations by S07C are lower than those of S99 with a maximum difference as high as 20 percent. The two mechanisms also show significant differences in the predicted OH, PAN, HCHO and HNO3 concentrations. Although the two mechanisms predict different ozone concentrations, the relative response factors (RRFs) of O3 at rural, urban and industrial sites under emission controls of anthropogenic NOx and VOC by factors 0.6 – 1.4 predicted by the two mechanisms are very similar. Predicted O3 concentrations by MCM are similar to those of SAPRC07. The MCM predicted total VOC OH reactivity is similar to the SAPRC07 predictions at a suburban site where biogenic emissions dominate the OH reactivity and is slightly lower than the SAPRC07 predictions at an industrial site where anthropogenic emissions dominate. Besides, the predicted 1-hr and 24-hr average concentrations of major O3 precursor VOCs by MCM show under predictions of alkanes and alkenes by a factor of 2-5, 6 for ethane and 8.5 for propane. Major aromatic compounds generally agree better with observations, although benzene is under-predicted by 80 percent. Species specific emission adjustment factors can be derived from these direct comparisons to improve emission inventories in future studies. At the Clinton Drive site, most of the under-predictions occur in the afternoon when industrial facilities are in the immediate upwind direction and the missing industrial emissions are likely evaporative sources whose emission rates are temperature dependent.