The emitting light in fireflies or other bioluminescent species arises from the electronic relaxation of oxyluciferin, an organic compound resulting from the oxidation of the D-luciferin substrate inside an enzyme called luciferase. These systems are already used in applications such as cell cancer detection. One of the challenges of the modelling of such systems, like other biological photoreceptor, is to reproduce the experimental absorption, fluorescence and emission spectra in order to better interpret the experimental results. Here will be presented the methodologies that can be used to study the spectroscopic proprieties of bioluminescent systems using quantum mechanics, molecular dynamics and hybrid (QM/MM) methods. The experimental emission and absorption spectra are accurately reproduced when the dynamic of the system is taking into account. Information of the nature of the transition can be taken from the modelling and insight of the influence of the protein environment can be highlighted.