Flocculation method in Surface Enhanced Raman Scattering (SERS) is elucidated to utilize coupled localized surface plasmon between closely adjacent metal nanoparticles towards single molecule characterization. In particular focus is placed on the distinct adsorption of cationic and neutral R123 and R6G molecules on Au nanoparticles (AuNPs), which are covered with much less amount of surface residuals than Ag nanoparticles (AgNPs). Indeed, the cationic dye molecules adsorb on AuNPs via electrostatic interaction with negatively charged metal surfaces, whereas neutral dye molecules adsorb via coordination bonds via lone pair electrons at nitrogen atoms in a tilted orientation. Flocculates of AgNPs were also formed using p-mercaptobenzoic acid (PMBA), providing enormous enhancement in surface enhanced Raman scattering. Electrostatic interaction between dissociated PMBA and counter ions, as well as van der Waals force between protonated PMBAs on AgNPs plays a crucial role in the flocculation. Mono- and divalent cations modified the ν_COO⁻ band at 1420 cm⁻¹ by 20 cm⁻¹ indicating distinct interaction of the hydrated cations with carboxylate anions of PMBA on AgNPs.