Single-molecule surface-enhanced Raman spectroscopy (SMSERS) of crystal violet (CV) has been reported since 1997, yet others have offered alternative explanations that do not necessarily imply SMSERS. Recently, the isotopologue approach, a statistically significant method to establish SMSERS, has been implemented for members of the rhodamine dye family. We provide the first demonstration of SMSERS of a triphenylmethane dye using the isotopologue approach. Two isotopologues of CV are employed to create chemically identical yet vibrationally distinct probe molecules. Experimental spectra were compared extensively with computational simulations to assign changes in mode frequencies upon deuteration. More than 90 silver nanoparticle clusters dosed with a 50:50 mixture of CV isotopologues were spectroscopically characterized, and the vibrational signature of only deuterated or undeuterated CV was observed 79 times, demonstrating that the isotopologue approach for proving SMSERS is applicable to both the CV and the rhodamine systems. The use of CV, a minimally fluorescent dye, allowed direct evaluation of enhancement factors (EF), which are reported herein. Through experiment and theory, we show that molecular electronic resonance Raman (RR) and surface-enhanced Raman effects combine synergistically in SMSERS. Excluding RR effects, the EFSERS is similar to 10(9). Variations and relationships between substrate morphology and optical properties are further characterized by correlated SMSERS-localized surface plasmon resonance (LSPR)-high-resolution transmission electron microscopy (HRTEM) studies. We did not observe SMSERS from individual nanoparticles; further, SMSERS-supporting dimers are heterodimers of two disparately sized particles, with no subnanometer gaps. We present the largest collection to date of HRTEM images of SMSERS-supporting nanoparticle assemblies.