Embodiments of an ultra-stable frequency reference generating system and methods for generating an ultra-stable frequency reference using a two-photon Rubidium transition are generally described herein. In some embodiments, a cavity-stabilized reference laser comprising a laser source is locked to a stabilized cavity. A Rubidium cell is interrogated by a stabilized laser output to cause at least a two-photon Rubidium transition and a detector may detect fluorescence resulting from spontaneous decay of the upper state Rubidium transition. The output of the detector is provided at a wavelength of the fluorescence to lock the cavity-stabilized reference laser to generate a stabilized laser output. A frequency comb stabilizer may be locked to the stabilized laser output to generate a super-continuum of optical wavelengths for use in generating an ultra-stable frequency reference.