Circadian rhythms are a universal way for organisms, ranging from prokaryotes to humans, to maintain coordination with the daily changes of light and temperature. It is known that a functional circadian clock confers enhanced fitness. In both animals and plants, diverse physiological processes are affected by the clock and more than 10% of transcripts show a circadian rhythm. Recent advances in the field have revealed a link between circadian regulated gene expression and dynamic changes in chromatin. Jumonji C (JmjC) domain-containing proteins have been shown to be involved in chromatin remodeling, acting as histone demethylases. The recent discovery that a JmjC-domain containing protein functions as a novel clock component suggests that histone modification has evolved as an important mechanism at the core of the circadian machinery.