A stepwise surface functionalization methodology was applied to nanostructured ZnO films grown by metal organic chemical vapor deposition (MOCVD) having three different surface morphologies (i.e., nanorod layers (ZnO films-N), rough surface films (ZnO films-R), and planar surface films (ZnO films-P). The films were grown on glass substrates and on the sensing area of a quartz crystal microbalance (nano-QCM). 16-(2-Pyridyldithiol)-hexadecanoic acid (PDHA) was bound to ZnO films-N, -R, and -P through the carboxylic acid unit, followed by a nucleophilic displacement of the 2-pyridyldithiol moiety by single-stranded DNA capped with a thiol group (SH-ssDNA). The resulting ssDNA-functionalized films were hybridized with complementary ssDNA tagged with fluorescein (ssDNA-Fl). In a selectivity control experiment, no hybridization occurred upon treatment with non complementary DNA. The ZnO films' surface functionalization, characterized by FT-IR-ATR and fluorescence spectroscopy and detected on the nano-QCM, was successful on films-N and -R but was barely detectable on the planar surface of films-P.