Significance Distinguishing the effects of light and sugars in photoautotrophic cells is challenging. The circadian system is a regulatory network that integrates light and metabolic signals and controls rhythmic physiology and growth. Our experimental approach has defined a light-independent, sugar-regulated transcriptome in Arabidopsis and revealed reactive oxygen species (ROS) as a prominent feature. ROS are byproducts of photosynthetic metabolism and oscillate with circadian rhythms but have not previously been demonstrated as inputs to the plant circadian oscillator. Our data suggest a role for superoxide as a rhythmic sugar signal which acts in the evening and affects circadian gene expression and growth.