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We propose the heterojunction effect in the analysis of the fluorescence mechanism of the firefly chromophore. Following this analysis, and with respect to the HOMO−LUMO gap alignment between the chromophore’s functional fragments, three main heterojunction types (I, II, and I*) are identified. Time-dependent density functional theory optical absorption calculations for the firefly chromophore show that the strongest excitation appears in the deprotonated anion state of the keto form. This can be explained by its high HOMO−LUMO overlap due to strong bioheterojunction confinement. It is also found that the nitrogen atom in the thiazolyl rings, due to its larger electronegativity, plays a key role in the emission process, its importance growing when the HOMO and LUMO overlap at its location. This principle is applied to enhance the chromophore’s fluorescence efficiency and to guide the functionalization of molecular optoelectronic devices.