Provided are multi-wavelength phototherapy systems and methods for the treatment of a disorder or disease, including multi-wavelength low level light therapy (“LLLT”), in particular to multi-wavelength LLLT and other phototherapy systems and methods for improving functionality in and/or restoring functionality to a cell and/or tissue through the coordinated and targeted delivery to the cell or tissue of two or more doses of light having distinct wavelengths, wherein the two or more doses of light, when delivered in a coordinated fashion, can stimulate the activity of two or more light sensitive factors that, when activated, provide and/or enhance a desired target cell functionality. Also provided are multi-wavelength phototherapy systems and methods for treatment of disorders and diseases that are associated with a diminished functionality in a cell of a patient afflicted with the disorder or disease, which can be adapted for therapeutic use by the coordinated and targeted delivery of two or more distinct wavelengths of light to a cell or tissue in a patient afflicted with a disorder and/or disease to restore or enhance, respectively, a diminished functionality to a cell and/or tissue that is associated with the disorder and/or disease healing the disorder or reversing and/or slowing the progression of one or more aspect of the disorder and/or disease. Within certain aspects, provided are multi-wavelength phototherapy systems and methods for the treatment of a damaged or diseased ocular tissue in an eye of a human, including ocular tissue that is associated with dry macular degeneration, which systems and methods include the delivery to the eye of two or more therapeutically effective doses of light, wherein the two or more therapeutically effective doses of light include a first dose of light having a first wavelength and a second dose of light having a second wavelength. These multi-wavelength phototherapy systems and methods can be used advantageously in combinat
