The self-assembled monolayers (SAMs) of the three isomers of aminothiophenol, ATP, have been studied by means of electrochemistry, in-situ STM and XPS. We find that the isomers are organized differently. The organization is presumably governed by their intermolecular and surface interactions. Moreover, the chemical and physical characteristics of the interface are significantly and differently affected by the isomers comprising the SAMs. The electrochemistry of the modified surface as well as the bare gold surface in contact with the thiol-containing electrolyte, copper deposition and palladium(II) extraction have been studied for the 2-, 3- and 4-ATP monolayers. The organization of the layers has been investigated by STM. In essence, we find that the different isomers are likely to adopt an orientation that is perpendicular to the surface. While 4-ATP forms the densest monolayer, 2-ATP probably interacts with the gold surface with both the amino and the mercapto groups. Moreover, STM images indicate the partial formation of more than a monolayer. This is supported by XPS measurements and electrochemistry and can be attributed to the SAM modification solution, i.e. sulfuric acid, which allows the formation of sulfate-bridged ATP bilayers. The chemical and physical characteristics of the interfaces are governed by the different organization as well as by the individual chemical properties of each isomer.