Indium tin oxide (ITO) is an attractive substrate for single-molecule electronics since it is transparent while maintaining electrical conductivity. Although it has been used before as a contacting electrode in single-molecule electrical studies, these studies have been limited to the use of carboxylic acid terminal groups for binding molecular wires to the ITO substrates. There is thus the need to investigate other anchoring groups with potential for binding effectively to ITO. With this aim, we have investigated the single-molecule conductance of a series of eight tolane or “tolane-like” molecular wires with a variety of surface binding groups. We first used gold-molecule- gold junctions to identify promising targets for ITO selectivity. We then assessed the propensity and selectivity of carboxylic acid, cyanoacrylic acid, and pyridinium-squarate to bind to ITO and promote the formation of molecular heterojunctions. We found that pyridinium squarate zwitterions display excellent selectivity for binding to ITO over gold surfaces, with contact resistivity comparable to that of carboxylic acids. These single-molecule experiments are complemented by surface chemical characterization with X-ray photoelectron spectroscopy, quartz crystal microbalance, contact angle determination, and nanolithography using an atomic force miscroscope. Finally, we report the first density-functional theory calculations involving ITO electrodes to model charge transport through ITO-molecule-gold heterojunctions.