The Au–S interface of thiol-based, self-assembled monolayers grown on Au(111) surfaces is far less understood than it should be. Local barrier height imaging, which has recently resolved work function variations in the buried interface of alkanethiolate monolayers, is now used to study self-assembled monolayers on Au(111) formed by cyclohexanethiol, a molecule with a flexible aliphatic ring structure. Multiple ordered phases are observed, consistent with its conformational flexibility which makes multiple interadsorbate interactions possible. In one particular phase, the appearance of two readily distinguishable features in local barrier height images implies at least two types of adsorption sites. Correlation of simultaneously acquired topographic and local barrier height data allows for a preliminary structural model that accounts for adsorption geometry.