Most frog species rely on vision as both tadpoles and adults, and thus the visual system changes to function optimally in the different light environments they inhabit across ontogeny. At metamorphosis, the eyes typically change size and position, along with changes in retinal circuitry, morphology, and sensitivity. The genomic basis of these changes, however, is poorly understood. We used whole eye transcriptome sequencing to investigate differential expression between aquatic tadpoles and terrestrial juveniles of the southern leopard frog and the effect that short-term (12h) exposure to light or darkness has on expression patterns. We found that many genes were differentially expressed in the eyes of tadpoles versus juveniles, while light/dark exposure had a relatively minor effect. Analyses targeting visual genes revealed significant differential expression between life stages in genes that control aspects of visual function and development including spectral sensitivity and lens composition. Light/dark exposure had a significant effect on a small subset of visual genes. Finally, microspectrophotometry of photoreceptors confirmed shifts in spectral sensitivity predicted by the expression results. Overall, we identified extensive expression-level differences in the eyes of tadpole and juvenile frogs that likely underlie observed morphological and physiological changes through metamorphosis and corresponding adaptive shifts to optimize visual ability in aquatic versus terrestrial light environments.