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Ionic liquids (ILs) are a promising alternative to the traditional organic solvents, but their toxic effects cause significant adverse environmental effects and their toxicity assessment have been suggested. The effect of the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([Bmim][BF4]) on photosynthesis was studied in Arabidopsis thaliana. Apparent effects on chlorosis and inhibition of photosynthetic capacity were observed. As [Bmim][BF4] concentrations increased, a time-dose effect was also observed. The maximum quantum yield (Fv/Fm), and the actual quantum yield of photosystem II (ΦPSII), both decreased; at the same time, the expression of psbA, a key gene of the photosystem II electron transport, was reduced by [Bmim][BF4] treatment. The synthesis of the large and small subunits of Rubisco were not affected by treatment. On the other hand, Rubisco activase (RCA) was significantly suppressed at the transcriptional level. Our results suggest that photochemistry of PSII as well as Rubisco activation are involved in ILs resistance. [ABSTRACT FROM AUTHOR]