The controlled electrodeposition of functional polydopamine (PDA) thin films from aqueous dopamine solutions is demonstrated with a combination of electrochemistry, atomic force microscopy (AFM), and surface plasmon resonance (SPR) measurements. PDA micropatterns are then fabricated by electrodeposition on micrometer length scale gold electrodes and used for attaching amino-modified single-stranded DNA (ssDNA). After hybridization with fluorescently labeled ssDNA, the fluorescence microscopy characterization reveals that: (i) PDA can be toposelectively deposited at the microscale and (ii) electrochemically deposited PDA can be functionalized with amino-terminated ssDNA using the same chemistry as that for spontaneously deposited PDA. Finally, the application of electrodeposited PDA thin films to fabricate ssDNA microarrays is reported using SPR imaging (SPRI) measurements for the detection of DNA and DNA-modified gold nanoparticles.