AbstractBlue light modulates many processes in plants and plant cells. It influences global and long‐term responses, such as seedling development and phototropism, and induces short‐term adaptations like stomatal opening and chloroplast movement. Three genes were identified as important for the latter process, namely PHOT1, PHOT2 and CHUP1. The former two phototropin blue light receptors act in perception of the blue light signal. The protein CHUP1 is localised to the outer envelope membrane of chloroplasts and is involved in chloroplast movement. To explore whether short‐term reactions required for chloroplast movement are under transcriptional control, we analysed the transcriptome in wild‐type Arabidopsis thaliana, phot1, phot2 and chup1 with different blue light treatments for 5 or 30 min. Blue light‐induced changes in transcription depended on illumination time and intensity. Illumination with 100 μmol·m−2·s−1 blue light induced down‐regulation of several genes and might point to cascades that could be important for sensing low levels of blue light. Analysis of the transcriptome of the mutants in response to the different light regimes suggests that the transcriptional response to blue light in the wild‐type can be attributed to phot1 rather than phot2, suggesting that blue light‐induced alteration of expression is a function of phot1. In contrast, the blue light response at the transcriptional level of chup1 plants was unique, and confirmed the higher light sensitivity of this mutant.