Received; accepted – 2 – Among the hot Jupiters that transit their parent stars known to date, the two best candidates to be observed with transmission spectroscopy in the mid-infrared (MIR) are HD189733b and HD209458b, due to their combined characteristics of planetary density, orbital parameters and parent star distance and brightness. Here we simulate transmission spectra of these two planets during their primary eclipse in the MIR, and we present sensitivity studies of the spectra to the changes of atmospheric thermal properties, molecular abundances and C/O ratios. Our model predicts that the dominant species absorbing in the MIR on hot Jupiters are water vapor and carbon monoxide, and their relative abundances are determined by the C/O ratio. Since the temperature profile plays a secondary role in the transmission spectra of hot Jupiters compared to molecular abundances, future primary eclipse observations in the MIR of those objects might give an insight on EGP atmospheric chemistry. We find here that the absorption features caused by water vapor and carbon monoxide in a cloud-free atmosphere, are deep enough to be observable by the present and future generation of space-based observatories, such as Spitzer Space Telescope and James Webb Space Telescope. We discuss our results in light of the capabilities of these telescopes
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