We report new near ultraviolet HST/STIS observations of atmospheric absorptions during the planetary transit of HD209458b. We detect absorption in atomic magnesium (MgI), while no signal has been detected in the lines of singly ionized magnesium (MgII). We measure the MgI atmospheric absorption to be 6.2+/-2.9% in the velocity range from -62 to -19 km/s. The detection of atomic magnesium in the planetary upper atmosphere at a distance of several planetary radii gives a first view into the transition region between the thermosphere and the exobase, where atmospheric escape takes place. We estimate the electronic densities needed to compensate for the photo-ionization by dielectronic recombination of Mg+ to be in the range of 10^8-10^9 cm^{-3}. Our finding is in excellent agreement with model predictions at altitudes of several planetary radii. We observe MgI atoms escaping the planet, with a maximum radial velocity (in the stellar rest frame) of -60 km/s. Because magnesium is much heavier than hydrogen, the escape of this species confirms previous studies that the planets atmosphere is undergoing hydrodynamic escape. We compare our observations to a numerical model that takes the stellar radiation pressure on the MgI atoms into account. We find that the MgI atoms must be present at up to ~7.5 planetari radii altitude and estimate an MgI escape rate of ~3x10^7 g/s. Compared to previous evaluations of the escape rate of HI atoms, this evaluation is compatible with a magnesium abundance roughly solar. A hint of absorption, detected at low level of significance, during the post-transit observations, could be interpreted as a MgI cometary-like tail. If true, the estimate of the absorption by MgI would be increased to a higher value of about 8.8+/-2.1%.
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