The electronic and crystallographic structure of the graphene/Rh(111) moiré lattice is studied via combination of density-functional theory calculations and scanning tunneling and atomic force microscopy(STM and AFM). Whereas the principal contrast between hills and valleys observed in STM does not depend on the sign of applied bias voltage, the contrast in atomically resolved AFM images strongly depends on the frequency shift of the oscillating AFM tip. The obtained results demonstrate the perspectives of application atomic force microscopy/spectroscopy for the probing of the chemical contrast at the surface.