Atomic hydrogen loss at the top of HD 209458bs atmosphere has been recently detected Vidal-Madjar et al. 2003. We have developed a 1-dimensional model to study the chemistry in the upper atmosphere of this extrasolar hot jupiter. The 3 most abundant elements (other than He), as well as 4 parent molecules are included in this model, viz., H, C, O, H2, CO, H2O, and CH4. The higher temperatures (~ 1000 K) and higher stellar irradiance (~6x10^5 W m^{-2}) strongly enhance and modify the chemical reaction rates in this atmosphere. Our two main results are that (a) the production of atomic hydrogen in the atmosphere is mainly driven by H2O photolysis and reaction of OH with H2, and is not sensitive to the exact abundances of CO, H2O, and CH4, and (b) H2O and CH4 can be produced via the photolysis of CO followed by the reactions with H2.