Visualization of the internal structures of the retina is critical for clinical diagnosis and monitoring of pathology as well as for medical research investigating the root causes of retinal degeneration. Optical Coherence Tomography (OCT) is emerging as the preferred technique for non-contact sub-surface depth-resolved imaging of the retina. The high resolution cross sectional images acquired in vivo by OCT can be compared to histology to visually delineate the retinal layers. The recent demonstration of the significant sensitivity increase obtained through use of Fourier domain (FD) detection with OCT has been used to facilitate high speed scanning for volumetric reconstruction of the retina in software. The images acquired by OCT are purely structural, relying on refractive index differences in the tissue for contrast, and do not provide information on the molecular content of the sample. We have constructed a FDOCT prototype and combined it with a fluorescent Scanning Laser Ophthalmoscope (fSLO) to permit real time alignment of the field of view on the retina. The alignment of the FDOCT system to the specimen is crucial for the registration of measurements taken throughout longitudinal studies. In addition, fluorescence detection has been integrated with the SLO to enable the en face localization of a molecular contrast signal, which is important for retinal angiography, and also for detection of autofluorescence associated with some forms of retinal degeneration, for example autofluorescence lipofuscin accumulations are associated with Stargardt's Macular Dystrophy. The integrated FD OCT/fSLO system was investigated for imaging the retina of the mice in vivo.