Remote observations by the Mariner10 and MESSENGER spacecraft have shown the existence of hydrogen in the exosphere of Mercury. However, to date the hydrogen number densities could only be estimated indirectly from exospheric models, based on the remotely observed Lyman-alpha radiances for atomic hydrogen (H), and the detection threshold of the Mariner10 occultation experiment for molecular hydrogen (H_2). Here we show the first on-site determined altitude-density profile of atomic H, derived from in-situ magnetic field observations by MESSENGER. The results reveal an extended H exosphere with densities that are ~1-2 orders of magnitude larger than previously predicted. Using an exospheric model that reproduces the H altitude-density profile, allows us to constrain the so far unknown H_2 density at the surface which is ~2-3 orders of magnitude smaller than previously assumed. These findings demonstrate the importance (1) of dissociation processes in Mercury’s exosphere and (2) of in-situ measurements giving complementary evidence of processes to remote observations, that will be realized in the near future by the BepiColombo mission.