1,8-Bis(5-mercaptomethyl-2-thienyl)octane (1a) 1,8-bis(5’-mercaptomethyl-2,2’-bithienyl-5-yl)octane (1b), 1-(5-mercaptomethyl-2-thienyl)-4-(2-thienyl)butane (1c), 1,8-bis(2,2’-bithienyl-5-yl)octane (2), 1,12-dodecanedithiol (3), and 1,4-bis(mercaptomethyl)benzene (4) were prepared, and their adsorption states on a gold single crystal surface were studied by using scanning tunneling microscopy under ultrahigh-vacuum condition. Two ordered phases were observed for the mercaptomethylthiophene derivatives 1 : The first phase is composed of one-dimensional molecular rows with spacings smaller than those for other monothiols and the second one has a previously unknown two-dimensional honeycomb structure. In both of the two phases, the molecules were arranged with end-on configuration in which only one end thiol is attached to the gold substrate. The absence of the honeycomb structure for 3 and 4 suggests the important role of the mercaptomethylthienyl moiety for the formation of the specific structures.