PURPOSE: To systematically and longitudinally investigate the characteristics of flecks in ABCA4-related retinopathy under different fundus autofluorescence (AF) excitation and emission spectra. METHODS: A total of 132 eyes of 66 patients with ABCA4-related retinopathy were investigated using multimodal AF imaging and spectral domain optical coherence tomography. Autofluorescence imaging with blue (BAF), green (GAF), and near-infrared (NIR-AF) excitation wavelengths obtained by a confocal scanning laser ophthalmoscope was compared with AF imaging obtained by an innovative confocal light-emitting diode-based retinal imaging system (Color-AF) that allows for separation of short (green emission fluorescent component) and long (red emission fluorescent component) autofluorescence emission components. RESULTS: Color-AF, BAF, and GAF, overall, revealed similar presentation of hyperautofluorescent flecks. Flecks that showed predominantly red emission fluorescent component matched with hyperautofluorescent flecks in NIR-AF. Over the observation time of 5 to 14 months, flecks showed a transition in the AF emission spectrum to shorter wavelengths (red emission fluorescent component to green emission fluorescent component), associated with a progressed disruption of overlaying outer retinal bands in optical coherence tomography. Newer hyperautofluorescent flecks usually revealed predominantly red emission fluorescent component. CONCLUSION: By separation of the AF spectra, the remodeling of fluorophores and associated structural changes can be monitored over time indicating a novel and susceptible surrogate marker for disease progression and potential therapeutic effects.