We have developed a pseudo two-dimensional model of a planetary atmosphere, which takes into account thermochemical kinetics, photochemistry, vertical mixing, and horizontal transport, the latter being modeled as a uniform zonal wind. We have applied the model to the atmospheres of the hot Jupiters HD 209458b and HD 189733b. The adopted eddy diffusion coefficients are calculated by following the behaviour of passive tracers in three-dimensional general circulation models, which results in eddy values significantly below previous estimates. We find that the distribution of molecules with altitude and longitude in the atmospheres of these two hot Jupiters is complex because of the interplay of the various physical and chemical processes at work. Much of the distribution of molecules is driven by the strong zonal wind and the limited extent of vertical transport, resulting in an important homogenisation of the chemical composition with longitude. In general, molecular abundances are quenched horizontally to values typical of the hottest dayside regions, and thus the composition in the cooler nightside regions is highly contaminated by that of warmer dayside regions. As a consequence, the abundance of methane remains low, even below the predictions of previous one-dimensional models, which is likely to be in conflict with the high CH4 content inferred from observations of the dayside of HD 209458b. Another consequence of the important longitudinal homogenisation of the abundances is that the variability of the chemical composition has little effect on the way the emission spectrum is modified with phase and on the changes in the transmission spectrum from the transit ingress to the egress, these variations in the spectra being mainly due to changes in the temperature rather than in the composition between the different sides of the planet.