We describe a novel technique for contrast enhancement in optical coherence tomography (OCT) which uses optically switchable protein based chromophores. Photosensitive proteins, such as bacteriorhodopsin and phytochrome, are promising OCT molecular contrast agents by reason of their remarkably low transition activation intensities compatible with in vivo imaging, and their potential for use as genetically expressible markers for molecular imaging. This study details the use of a novel optical switch suppression scheme which uses the absorption change between the two state groups of phytochrome to extract concentration and distribution information of the contrast agent within a target sample.