In situ electrochemical surface enhanced Raman spectra (SERS) for an immobilized monolayer of a flavin analogue (isoalloxazine) at nanostructured silver surfaces are reported. Unique in the present study, the flavin is not directly adsorbed at the Ag surface but is attached through a chemical reaction between cysteamine adsorbed on the Ag surface and methylformylisoalloxazine. Even though the flavin is held away from direct contact with the metal, strong surface enhancements are observed. The nanostructured silver surfaces are produced by electrodeposition through colloidal templates to produce thin (< 1 mu m) films containing close-packed hexagonal arrays of uniform 900 nm sphere segment voids. The sphere segment void (SSV) structured silver surfaces are shown to be ideally suited to in situ electrochemical SERS studies at 633 nm, giving stable, reproducible surface enhancements at a range of electrode potentials, and we show that the SER spectra are sensitive to subfemtomole quantities of immobilized flavin. Studies of the SER spectra as a function of the electrode potential show clear evidence for the formation of the flavin semiquinone at the electrode surface at cathodic potentials.