Organodithiols including para-aryl dithiols (PADTs, HS-(C6H4)n-SH, n = 1, 2 and 3) and alpha, omega-alkanedithiols (ADTs, HS-(CH2)n-SH, n = 2, 4, …) with two distal thiols have been used extensively in molecular electronics, surface-enhanced Raman spectroscopy (SERS), and quantum electron tunneling between two gold or silver nanoparticles (AuNPs and AgNPs). The popular belief is that these dithiols cross-link noble metal nanoparticles (NPs) as monolayer dithiolate spacers. Reported is the finding that PADTs predominantly exist as monothiolate forms on AuNPs or AgNPs. No PADT-induced NP cross-linking was observed regardless of NP/PADT concentration ratios. 1,4-benzenedimethanethiol (HS-CH2-(C6H4)-CH2-SH) and ADT can be completely deprotonated, forming dithiolates on AuNPs and AgNPs, while only one PADT thiol can be deprotonated even when PADTs are treated with concentrated NaOH or AgNO3. AuNP localized surface plasmon resonance (LSPR) measurement provides conclusive evidence that ADT in AuNP junctions primarily consisted of dithiolate monomers in which the two sulfides are either attached to the same AuNP, or cross-link two adjacent AuNPs as single-molecular spacers. However, ADT molecules most likely in the area surrounding the AuNP junction are monothiolate with their distal thiols either remaining intact or forming disulfide cross-links with neighboring adsorbed ADTs. The possibility for ADT to cross-link two AgNPs as single molecular linker is excluded on the basis of TEM measurements that showed ADT-induced AgNP disintegration. This work highlights the difference between organothiol interactions with AgNPs and AuNPs and should be of broad importance for plasmonic NP research given the popularity of PADTs in molecular electronics and SERS applications.