Optically triggered twisted intramolecular charge transfer (TICT) states in donor–acceptor chromophores form the molecular basis for designing bioimaging probes that sense polarity, microviscosity, and pH in vivo. However, a lack of predictive understanding of the “twist” localization precludes a rational design of TICT-based dyes. Here, using femtosecond stimulated Raman spectroscopy, we reveal a distinct Raman signature of the TICT state for a stilbazolium-class mitochondrial staining dye. Resonance-selective probing of 4-N,N-diethylamino-4″-N′-methyl-stilbazolium tosylate (DEST) tracks the excited-state structure of the dye as it relaxes to a TICT state on a picosecond time scale. The appearance of a remarkably blue-shifted C=C stretching mode at 1650 cm–1 in the TICT state is attributed to the “twist” of a single bond adjacent to the ethylenic π-bridge in the DEST backbone based on detailed electronic structure calculations and vibrational mode analysis. Our work demonstrates that the π-bridge, connecting the donor and acceptor moieties, influences the spatial location of the “twist” and offers a new perspective for designing organelle-specific probes through cogent tuning of backbone dynamics.