The synthesis and characterization of two-dimensional (2D) molecular crystals composed of long and linear phosphonic acids atop graphene is reported. Using scanning probe microscopy in combination with first-principles calculations, we show that these true 2D crystals are oriented along the graphene armchair direction only, thereby enabling an easy determination of graphene flake orientation. We have also compared the doping level of graphene flakes via Raman spectroscopy. The presence of the molecular crystal atop graphene induces a well-defined shift in the Fermi level, corresponding to hole doping, which is in agreement with our ab initio calculations.