We report a simple size focusing, two-step “bottom-up” protocol to prepare water-soluble Au25(MBA)18 nanoclusters, using the three isomers of mercaptobenzoic acids (p/m/o-MBA) as capping ligands and Me3NBH3 as a mild reducing agent. The relative stability of the gas-phase multiply deprotonated Au25(MBA)18 ions was investigated by collision-induced dissociation. This permitted us to evaluate the possible isomeric effect on the Au–S interfacial bond stress. We also investigated their optical properties. The absorption spectra of Au25(MBA)18 isomers were very similar and showed bands at 690, 470, and 430 nm. For all Au25(MBA)18 isomeric clusters, no measurable one-photon excited fluorescence under UV–vis light was found, in neither solid- nor solution-state. The two-photon excited emission spectra and first hyperpolarizabilities of the clusters were also determined. The results are discussed in terms of the possible isomeric effect on excitations within the metal core and the possibility of charge transfer excitations from the ligands to the metal nanocluster.