In the past 10 years, a lot of plant circadian rhythm researches have published in molecular biology and biochemistry. We discussed with published molecular studies of circadian clock and rhythmic genes in Arabidopsis, rice and algae. However past this studies are not sufficient to explain the whole rhythmic metabolism. Recently many researchers have concerned post-transcriptional, translational and post-translational modification of rhythmic proteins. From the view point of the high-throughput study, we could suggest the proteomic analysis with 2-DE gel electrophoresis and MS/MS techniques for the identification of modified proteins.