Alkanethiol adsorption on the Au(100) surfaces is studied by using scanning tunneling microscopy, X-ray photoelectron spectroscopy, and electrochemical techniques. Adsorption of hexanethiol (HT) on the Au(100)-hex surface results in the formation of elongated Au islands following the typical stripes of the reconstruction. Ordered molecular arrays forming hexagonally distorted square patterns cover the stripes with surface coverage approximate to 0.33. On the other hand, HT adsorption on the Au(100)-(1 X 1) surface shows the absence of the elongated island and the formation of square molecular patterns with a surface coverage approximate to 0.44. The core level shift of thiolates adsorbed on the Au(100)-(1 X 1) and Au(111) is only 0.15 eV, suggesting that chemistry rather than surface sites determines the binding energy of the S 2p core level. These results are also important to complete our knowledge of the chemistry and surface structure for small thiolated AuNPs where the Au(100) together with the Au(111) are the dominant faces.