The ability to pattern a surface locally with different molecular monolayers in a well-controlled fashion and at nanoscale resolution has importance for molecular electronics and biotechnology applications, as well as for nanoengineering. Here, we report a new technique for selectively functionalizing closely spaced gold electrodes of separation below 50 nm with different thiolated oligonucleotides using a local, selective electrochemical desorption of a molecular protection layer followed by the subsequent adsorption of the oligonucleotides onto the exposed surface. This technique does not rely on the use of a local probe such as an atomic force microscope tip. We furthermore show that the surface-bound oligonucleotides retain their unique molecular recognition and self-assembly properties and so functionalize the electrode array.