Abstract: The growth of nanocrystal superlattices of 5 nm single domain Au nanocrystals at an air-toluene interface induces formation of well-defined thin films (300–400 nm) with large coherence lengths. High-resolution electron microscopy showed that polyhedral holes (negative supracrystal) were formed on the nanocrystal superlattice surface. Formation of negative supracrystals is attributed to inclusion in the superlattice of organic molecules (dodecanethiol), which are present in concentrated zones at the air-toluene interface. The coexistence of two supracrystalline structures (bcc/fcc) is attributed to diffusion of dodecanethiol molecules resulting in a Bain deformation of the nanocrystal array.