<h4>Background</h4>It is now well documented that moonlight affects the life cycle of invertebrates, birds, reptiles, and mammals. The lunisolar tide is also well-known to alter plant growth and development. However, although plants are known to be very photosensitive, few studies have been undertaken to explore the effect of moonlight on plant physiology.<h4>Results</h4>Here for the first time we report a massive transcriptional modification in Coffea arabica genes under full moonlight conditions, particularly at full moon zenith and 3 h later. Among the 3387 deregulated genes found in our study, the main core clock genes were affected.<h4>Conclusions</h4>Moonlight also negatively influenced many genes involved in photosynthesis, chlorophyll biosynthesis and chloroplast machinery at the end of the night, suggesting that the full moon has a negative effect on primary photosynthetic machinery at dawn. Moreover, full moonlight promotes the transcription of major rhythmic redox genes and many heat shock proteins, suggesting that moonlight is perceived as stress. We confirmed this huge impact of weak light (less than 6 lx) on the transcription of circadian clock genes in controlled conditions mimicking full moonlight. Conclusions Moonlight also negatively influenced many genes involved in photosynthesis, Artificial lighting (also sometimes referred to as light pollution) alters natural light regimes (spatially, temporally, and spectrally), when light is perceived as an information source and not as a resource [ 11 , 12 ]. Kadman-Zahavi and Peiper (1987) reported that, in their experimental conditions, plants exposed to moonlight flowered 2–3 days late. They suggested that, while full moonlight may be perceived in the photoperiodic reaction, in the natural environment it would only have a very slight effect on the time of flower induction at the most [ 13 ]. To further investigate this discovery, we analyzed our samples using RNAseq and confirmed our results at spring solstice in plants grown under the same environmental conditions, but also in plants grown in a phytotron. Results Particularities of moonlight Different communities worldwide traditionally use lunar rhythms as a tool to pinpoint the best germination and harvest times. The moon can act in two ways on plants, via its gravitational effect or via the sunlight it reflects. The gravitational effect is now well known, but the effect of full moon (FM) light is completely unknown. Despite the difficulty in reproducing the light of the FM, after 7 days of treatment, plants exposed to this artificial ‘moonlight’ showed atypical transcription at ZT21 of LHY , PHOT1 and PHOT2 genes in the RT-qPCR analysis (Fig. 5 ). The night peak was produced at ZT21 instead of ZT15 under natural FM conditions. Fig. 5 Spectrometer measurements on a NM day, a full sun day and in a growth chamber. We simulated the luminous intensity of the moon in a growth chamber using four types of LED programmed at the main wavelengths 450 nm (blue), 660 nm (red), 730 nm (red) and in white light to emit a light intensity of 6 lx (< 2 PAR). It is likely that several of these photoreceptors are involved in moonlight perception. At the transcription level, most of them were unaffected, except phototropins, which were highly expressed at the FM zenith. Phototropins are blue-light receptors controlling a range of responses that serve to optimize the photosynthetic efficiency of plants. These include phototropism, light-induced stomatal opening, and chloroplast movements in response to changes in light intensity [ 23 ]. Photoreceptors and metabolites produced during photosynthesis, operate to synchronize the internal timing clock with lighting cues. In our study, we hypothesized that massive transcriptional activation would be a good way to demonstrate the effect of moonlight on plants. Moreover, transcript abundance is useful to assess the effects of external clues on circadian oscillations. Light-regulated changes in the morphology of a dicot or monocot seedling are accompanied by an alteration in the expression of up to 20% genes in Arabidopsis and rice [ 24 ]. Here we hypothesize that, once a plant has perceived moonlight, ribosomal genes and PPR proteins serve as regulatory factors and reprogram nuclear and organellar gene expression earlier. Regarding photosynthesis-related genes, 50 genes of this pathway were deregulated by moonlight. Many of these genes were found to be down-regulated just before and at dawn, suggesting that full moonlight has a negative effect on the primary photosynthetic machinery at dawn. We demonstrated that the weak intensity of the FM was able to alter the transcription of many important genes. However, it is still unclear how this transcription alteration is translated phenotypically. During the FM, samples were also taken from control plants cultivated in a phytotron under artificial light (CRYONEXT, model RTH 1200 L, with the following parameters: 12/12 h light/dark photoperiod, 80% humidity, 25 °C temperature and 600 mmol m − 2 s − 1 luminosity. We performed an experiment using the same phytotron and conditions to identify the set of genes with rhythmic expression. We generated a 48 h transcriptomic time-course dataset. Leaves were snap frozen in liquid nitrogen and stored at − 80 °C until RNA analysis. During sampling, three biological replicates were performed using three plants for all RNAseq experiments and four biological replicates with the plants exposed to simulated moonlight. To classify the time points at which the sampling was carried out, we used Zeitgeber time (ZT), which is defined as the time in hours from the start of a normal 12/12 h photoperiod cycle (photoperiod 12 h/12 h). For this purpose, we collected leaf samples at 3 h resolution from ZT0 to ZT24. Light analysis Solar and lunar light was analyzed in 2016 and 2017 at spring solstice using an MR-16v4 Rainbow - Light Portable Light Measuring Instrument.