A simple, inexpensive direct micromolding method for patterning Au nanocrystal superlattices using a polydimethylsiloxane (PDMS) stamp has been developed. The method involves in situ synthesis of Au(I) dodecanethiolate and its decomposition leading to Au nanocrystals in the microchannels of the stamp which order themselves to form patterned superlattice stripes, in conformity with the stamp geometry. Owing to its insolubility in common solvents, the dodecanethiolate was made by reacting Au(PPh3)Cl and dodecanethiol in situ inside the microchannels, by injecting first the former solution in toluene at room temperature followed by the thiol solution at 120 °C. Annealing the reaction mixture at 250 °C, resulted in formation of nanocrystals (with a mean diameter of 7.5 nm) and hexagonal ordering. By using an external pressure while molding, parallel stripes with sub-100 nm widths were obtained. The choice of parameters such as injection temperature of the thiol and concentrations is shown to be important if an ordered superlattice is to be obtained. In addition, these parameters can be varied as a means to control the nanocrystal size.