Understanding the structure and conductance of the molecular junction between benzene dithiolates (BDT) and gold electrodes has posed a classic unsolved problem for high-level theoretical work for over a decade. Recent breakthroughs for the gold−thiolate interface in thiolate-passivated gold clusters and in Au(111)/self-assembled monolayers (SAMs) motivated us to reanalyze the properties of Au−BDT−Au junctions. We show that distinct molecular Au(SR)2 and Au2(SR)3 units, which are known to exist at the nanoparticle−thiolate and Au−SAM interfaces, define the properties of the electrode−molecule junction. These units can form multiple contacts. The junction can be stretched by more than 1 nm whereby alternating gold−thiolate chains are spontaneously formed in ab initio molecular dynamics simulations. The calculated conductance values for the BDT junctions agree with a wide range of reported experimental data. Our results give a solid ground for further theoretical studies of molecular junctions between gold and a wide variety of organic molecules containing dithiols.