We show that highly ordered two-dimensional (2D) chessboard arrays consisting of a periodic arrangement of two different molecules can be obtained by self-assembly of unsubstituted metal–phthalocyanines (metal-Pcs) on a suitable substrate serving as the template. Specifically, CuPc + MnPc and CuPc + CoPc mixtures sort into highly ordered Cu/Mn and Cu/Co chessboard arrays on the square p(10 × 10) reconstruction of bismuth on Cu(100). Such created bimolecular chessboard assemblies emerge from the site-specific interactions between the central transition-metal ions and the periodically reconstructed substrate. This work provides a conceptually new approach to induce 2D chessboard patterns in that no functionalization of the molecules is needed.