The structure of a physisorbed sub-monolayer of 1,2-bis(4-pyridyl)ethylene (bpe) on epitaxial graphene is investigated by Low-Energy Electron Diffraction and Scanning Tunneling Microscopy. Additionally, non-equilibrium heat-transfer between bpe and the surface is studied by Ultrafast Low-Energy Electron Diffraction. Bpe arranges in an oblique unit cell which is not commensurate with the substrate. Six different rotational and/or mirror domains, in which the molecular unit cell is rotated by 28±0.1 with respect to the graphene surface, are identified. The molecules are weakly physisorbed, as evidenced by the fact that they readily desorb at room temperature. At liquid nitrogen temperature, however, the layers are stable and time-resolved experiments can be performed. The temperature changes of the molecules and the surface can be measured independently through the Debye-Waller factor of their individual diffraction features. Thus, the heat flow between bpe and the surface can be monitored on a picosecond timescale. The time-resolved measurements, in combination with model simulations, show the existence of three relevant thermal barriers between the different layers. The thermal boundary resistance between the molecular layer and graphene was found to be 2±1•10-8 K m 2 W-1. Received: ((will be filled in by the editorial staff)) Revised: ((will be filled in by the editorial staff))