Fluorophore tagged proteins are used in Arabidopsis thaliana to understand their functional role in plant development. This requires the analysis of their spatial localization in planta. However, the localization analysis is often perturbed by a significant overlap of the fluorophores used to label proteins of interest and the optical filtering methods available on the confocal microscope. This problem can be addressed by the use of spectral imaging with linear unmixing the image data. We applied this method to help us identify double transgenic A. thaliana lines which expressed two fluorescently tagged auxin transporter proteins: the auxin efflux protein PIN-FORMED-3 (PIN3), tagged with green fluorescent protein (GFP), and the auxin influx protein LIKE-AUX1-3 (LAX3), tagged with yellow fluorescent protein (YFP). This method allows the reliable separation of overlapping GFP and YFP fluorescence signals and subsequent localization analysis highlighting the potential benefit of this methodology in studies of lateral root development.