The use of Raman spectroscopy in biochemistry has been very successful, particularly because of its ability to identify elementary chemical species. However, application of this spectroscopic technique for in vivo assessment is often limited by autofluorescence, which make detection of Raman signatures difficult. The mouse eye has been used as an optical testbed for investigation of a variety of disease models and therapeutic pathways. Implementation of in vivo Raman spectroscopy in mice retina would be valuable but needs to be examined in context of the intrinsic auto-fluorescence artifact and potential light damage if high probing beam powers were used. To evaluate feasibility, a Raman system was built on a custom SLO/OCT platform allowing mouse positioning and morphological data acquisition along with the Raman signal from a desired retinal eccentricity. The performance of the Raman system was first assessed with a model eye consisting of polystyrene in the image plane (retina), using excitation wavelengths of 488 nm, 561 nm, and 785 nm to determine whether auto-fluorescence would be reduced at longer wavelengths. To improve the SNR, the combined system is featured with the optical compatibility for these three excitations such that their corresponding spectra from a typical region of interest can be acquired consecutively during single imaging run. Our results include emission spectra acquired over 10 s with excitation energy less than 160 J.s-1.m-2 for all wavelengths and corresponding retinal morphology for different mouse strains including WT, BALB/c and ABCA4-/-.