Alkanethiol self-assembled monolayers formed on Au(111) surfaces were investigated by noncontact atomic force microscopy (NC-AFM). Dodecanethiol monolayers prepared at 78 °C were imaged by NC-AFM, which revealed that the film is composed predominantly of two different phases of c(4×2) superlattice structures. The obtained molecular-scale NC-AFM contrasts are discussed in comparison with previously reported scanning tunneling microscopy images. We found that the energy dissipation image exhibits a clear difference in its molecular-scale contrast between the two phases. Possible origins of the difference are discussed in relation to the fluctuation and/or stability of the packing structures. © 2004 American Institute of Physics.