Abstract: Here, it is shown that binary superlattices of Co/Ag nanocrystals with the same size, surface coating, differing by their type of crystallinity are governed by Co–Co magnetic interactions. By using 9 nm amorphous-phase Co nanocrystals and 4 nm polycrystalline Ag nanocrystals at 25 °C, triangle-shaped NaCl-type binary nanocrystal superlattices are produced driven by the entropic force, maximizing the packing density. By contrast, using ferromagnetic 9 nm single domain (hcp) Co nanocrystals instead of amorphous-phase Co, dodecagonal quasicrystalline order is obtained, together with less-packed phases such as the CoAg13 (NaZn13-type), CoAg (AuCu-type), and CoAg3 (AuCu3-type) structures...