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ABSTRACT Miscanthusholds a promise as a biocrop due to its high yield, perenniality and ability to grow on infertile soils. However, the current commercial biomass production ofMiscanthusis mostly limited to a single sterile triploid clone ofM.×giganteus. Nevertheless, parental species ofM.×giganteus, MiscanthussacchariflorusandMiscanthussinensiscontain vast genetic diversity for crop improvement. WithM. sacchariflorushaving a natural geographic distribution in cold‐temperate northeast China and eastern Russia, we hypothesised that it has substantial variation in physiological response to chilling. Using a semi‐high‐throughput method, we phenotyped 209M. sacchariflorusgenotypes belonging to six genetic groups for non‐photochemical quenching (NPQ) and photosystem II efficiency (ΦPSII) kinetics under warm and chilling treatments in three growing seasons. In response to the chilling treatment, all genetic groups exhibited an increase in NPQ induction rate indicating faster activation of NPQ in light. Notably, under chilling, the Korea/NE China/Russia 2x and N China 2x groups stood out for the highest NPQ rate in light and the highest steady‐state NPQ in light. This NPQ phenotype may contribute adaptation to chilling during bright, cold mornings of spring and early autumn in temperate climates, when faster NPQ would better protect from oxidative stress. Such enhanced adaptation could expand the growing season and thus productivity at a given location or expand the range of economically viable growing locations to higher latitudes and altitudes. A genome‐wide association study identified 126 unique SNPs associated with NPQ and ΦPSII traits. Among the identified candidate genes were enzymes involved in the ascorbate recycle and shikimate pathway, gamma‐aminobutyric acid and cation efflux transporters. Identifying natural variation and genes involved in NPQ and ΦPSII kinetics considerably enlarges the toolbox for breeding and/or engineeringMiscanthuswith optimised photosynthesis under warm and chilling conditions for sustainable feedstock production for bioenergy. Chilling affects the productivity and geographical distribution of most crops. Using a semi‐high‐throughput approach to investigate photosynthesis‐related traits, we characterised variation existing in the bioenergy cropMiscanthusunder chilling and warm conditions and identified potential genes associated with it. Under chilling, two genetic groups from the northern edge ofMiscanthusdistribution stood out for faster activation of photoprotection. This trait may contribute adaptation to chilling in temperate climates, when faster photoprotection would better defend from oxidative stress. Enhanced chilling adaptation could expand the growing season and thus productivity or enlarge the range of growing locations.