Luciferin molecules are common luminophores found throughout the biological kingdoms. Here, electrospray ionization and tandem ion mobility spectrometry coupled with laser spectroscopy are used to demonstrate that D-luciferin and oxyluciferin deprotonated anions can be produced in two isomeric forms, which can be separated by virtue of their different collision cross sections with a buffer gas. The two isomers possess distinguishable but partially overlapping photodepletion action spectra over the visible range, implying distinct intrinsic absorption profiles. The site of deprotonation and tautomeric forms of the electrosprayed isomers are assigned through comparisons between experimental and calculated collision cross sections and electronic excitation energies. The study clearly shows that electrospray ionization of biochromophore molecules can generate multiple isomeric forms with distinct electronic spectra.