Provided are multi wavelength phototherapy devices systems and methods for the treatment of a disorder or disease including multi wavelength low level light therapy (PBM) in particular to multi wavelength PBM 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. Ophthalmic phototherapy devices systems and treatment methods to expose an eye to selected multi wavelengths of light to promote the healing of damaged or diseased eye tissue. The devices include a housing having an interior； an eyepiece disposed on the housing and configured and arranged for placement of an eye of the patient adjacent the eyepiece； a first light source producing a first light beam having a first therapeutic wavelength and disposed within the housing； a second light source producing a second light beam having a second therapeutic wavelength and disposed within the housing where the second therapeutic wavelength differs from the first therapeutic wavelength by at least 25 nm.
