In several mammalian species, the retina contains an autonomous circadian clock and is capable of synthesizing melatonin. The function of circadian clocks depends on interlocking transcriptional/translational feedback loops involving several clock genes. Here we investigated the expression of two clock genes (Per1, Cry2) and the level of phosphorylated (p) cyclic AMP response element binding protein (CREB) in retinae of melatonin-deficient (C57BL) with an intact retina and melatonin-proficient (C3H) mice with degenerated outer nuclear layer. RNase protection assay and in situ hybridization revealed in both strains a rhythm in transcript levels for Per1 with a peak at zeitgeber time (ZT) 08, but not for Cry2. Immunoreactions for PER1, CRY2 and pCREB were localized to the nuclei of cells in the inner nuclear layer (INL) and ganglion cell layer (GC) of both strains and to the outer nuclear layer of C57BL. In C3H, protein levels of PER1 and CRY2 followed a clear day/night rhythm in the INL and the GC with a peak at the end of the day (ZT14). pCREB levels peaked at the beginning of the day. Noteably, in melatonin-deficient C57BL mice, protein levels of PER1, CRY2 and pCREB did not show significant changes over a 16L/8D cycle. These data suggest that melatonin influences PER1 and CRY2 protein levels via post-transcriptional mechanisms and also plays a role in rhythmic regulation of pCREB levels in the mammalian retina.