We present a systematic study of the effect of methyl substitution on iso- and alloxazines in acetonitrile solutions. Substitution patterns have profound effects on both spectral and photophysical properties, with fluorescence quantum yields varying by more than an order of magnitude. TD-DFT calculation were used for the first time to correlate electronic structure changes with the substitution patterns, with good agreement between calculated and theoretical band positions and oscillator strengths. Both n-pi* and pi-pi* states in these compounds are predicted, with the oscillator strengths indicating that only the pi-pi* states should be observable in the absorption spectra. Substitution patterns are shown to be responsible for energy order inversion between these states.