Probing the crystallographic orientation of two-dimensional (2D) materials is essential to understand and engineer their properties. However, the nondestructive identification of the lattice orientations of various 2D materials remains a challenge due to their very thin nature. Here, we identify the crystallographic structures of various 2D atomic crystals using molecules as probes by utilizing orientation-dependent molecule-substrate interactions. We discover that the periodic atomic packing of 2D materials guides oleamide molecules to assemble into quasi-one-dimensional nanoribbons with specific alignments which precisely indicate the lattice orientations of the underlying materials. Using oleamide molecules as probes, we successfully identify the crystallographic orientations of ~12 different 2D materials without degrading their intrinsic properties. Our findings allow for the nondestructive identification of the lattice structure of various 2D atomic crystals and shed light on the functionalization of these 2D materials with supramolecular assembly.Identifying the crystallographic orientations of 2D materials is important, but methods to do so are typically destructive. Here, the authors show that the orientational dependency of self-assembled nanoribbons of oleamide molecules can be used to non-invasively probe the lattice orientations of various 2D substrates.