The self-assembly of cyanuric acid into ordered nanostructures on a crystalline substrate, highly ordered pyrolytic graphite (HOPG), has been investigated at low temperature under ultrahigh vacuum (UHV) conditions by means of scanning tunneling microscopy in conjunction with theoretical simulations. Many domains with different self-assembly patterns were observed. One such domain represents the formation of an open 2D rosette (cyclic) structure from the self-assembly process, the first observation of this type of structure for pure cyanuric acid on a graphite substrate. Each self-assembled domain exhibits characteristic superstructures formed through different hydrogen bond networks at low coverage and low deposition rate. Experimental observation of coexistent, two-dimensional crystalline structures with distinct hydrogen bond patterns is supported by energy minimizations and molecular dynamics calculations, which show multiple stable structures for this molecule when self-assembled on graphite.