The results of the search for the optimal experimental conditions for ultrasentitive chemical analysis of 1-naphthalenethiol (1-NAT) and 2-naphthalenethiol (2-NAT) using surface-enhanced Raman scattering (SERS) are discussed. The report begins with a review of the vibrational spectra, including infrared and Raman spectra of the target molecules, and the interpretation of the observed frequencies aided by local density functional theory (DFT) calculations at the B3LYP/6-311G(d,p) level of theory. Several metal nanostructures were tested for SERS activity, including island films and colloids of silver, gold and copper. Correspondingly, the most effective laser line for excitation in the visible and near infrared region was sought. The achieved detection limit for 1-naphthalenethiol, and for 2-naphthalenethiol, on silver nanostructures is in the zeptomole regime.