Context. A new class of exoplanets has emerged: the ultra hot Jupiters, the hottest close-in gas giants. The majority of them have weaker-than-expected spectral features in the 1.1−1.7 μ m bandpass probed by HST/WFC3 but stronger spectral features at longer wavelengths probed by Spitzer . This led previous authors to puzzling conclusions about the thermal structures and chemical abundances of these planets. Aims. We investigate how thermal dissociation, ionization, H − opacity, and clouds shape the thermal structures and spectral properties of ultra hot Jupiters. Methods. We use the SPARC/MITgcm to model the atmospheres of four ultra hot Jupiters and discuss more thoroughly the case of WASP-121b. We expand our findings to the whole population of ultra hot Jupiters through analytical quantification of the thermal dissociation and its influence on the strength of spectral features. Results. We predict that most molecules are thermally dissociated and alkalies are ionized in the dayside photospheres of ultra hot Jupiters. This includes H 2 O , TiO, VO, and H 2 but not CO, which has a stronger molecular bond. The vertical molecular gradient created by the dissociation significantly weakens the spectral features from H 2 O while the 4.5 μ m CO feature remains unchanged. The water band in the HST/WFC3 bandpass is further weakened by the continuous opacity of the H − ions. Molecules are expected to recombine before reaching the limb, leading to order of magnitude variations of the chemical composition and cloud coverage between the limb and the dayside. Conclusions. Molecular dissociation provides a qualitative understanding of the lack of strong spectral features of water in the 1−2 μ m bandpass observed in most ultra hot Jupiters. Quantitatively, our model does not provide a satisfactory match to the WASP-121b emission spectrum. Together with WASP-33b and Kepler-33Ab, they seem the outliers among the population of ultra hot Jupiters, in need of a more thorough understanding.