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Besides the prevalent well-established paradigms in the description of the excited-state relaxation in biological chromophores, like the cis-trans isomerization reactions, the uncommon nonradiative decay paths are at the focus of the current study. In particular, systems having low-lying dark excited states in their electronic spectrum represent the most important target group. Our results indicate the existence of a new type of nonradiative transition pathway in the subclass of novel photoacids - the green fluorescent protein synthetic chromophores such as meta-HBDI. Recently, action photoabsorption spectroscopy studies of the meta-HBDI anion in vacuum have revealed the presence of the dark state by its direct observation. The meta-anion electronic spectrum is characterized by the distinct π-π* transition of the charge-transfer character. The lowest-energy nearly dark S1 state originates from the one-electron excitation occurring between two isoelectronic π-systems, which are effectively decoupled due to the absence of the valence resonance structures in the meta-HBDI anion in the ground electronic state. Fast and efficient relaxation channel through a conical intersection between the bright and dark excited states is expected. The decay channel leads to the fast fluorescence quenching in the anion, whereas the excited state proton transfer is a non-adiabatic process in the neutral chromophore in water solution. The topographies around three conical intersections define the complexity of the excited-state dynamics. A life-time of the system in the excited state after crossing the first seam and a branching ratio of subpopulations with a distinct dark or bright electronic structure can be efficiently regulated by modifications of the local surrounding of the chromophore. A novel type of dark states can be found in other “meta-systems”.