The purpose of this study is to demonstrate the application of ultrahigh-resolution Spectral Domain Optical Coherence Tomography (SD-OCT) for non contact in vivo imaging of the retina of small animals and quantitative retinal information extraction using 3D segmentation of the OCT images. An ultrahigh-resolution SD-OCT system was specifically designed for in vivo retinal imaging of small animal. En face fondus image was constructed from the measured OCT data, which enables precise registration of the OCT images on the fondus. 3D segmentation algorithms were developed for the calculation of retinal thickness map. High quality OCT images of the retina of mice (B6/SJLF2 for normal retina, Rho-/- for photoreceptor degeneration and LH BETATAG for retinoblastoma) and rats (Wistar for normal retina) were acquired, where all the retinal layers can be clearly recognized. The calculated retinal thickness map makes successful quantitative comparison of the retinal thickness distribution between normal and degenerative mouse retina. The capabilities of the OCT system provide a valuable tool for longitudinal studies of small animal models of ocular diseases.