A simple approach to form arrays of covalently bonded single gold nanoparticles (AuNPs) is demonstrated. Asymmetric molecular assemblies composed of two layers of rigid aromatic molecules with different structures, arranged in hexagonal arrays on a template produced by edge-spreading lithography, are used to guide the assembly of AuNPs. Arrays of single AuNPs are achieved by taking advantage of the interplay of electrostatic interactions and covalent bonding in conjunction with the positional constraint on the template. Schiff base chemistry is highlighted in the surface chemical reaction to selectively modify nanoscale surface features with high yield.