There is increasing evidence for considerable interlinking between the responses to heat stress (HS) and light signaling. In the present work, we provide molecular evidence that BBX18, a negative regulator in photomorphogenesis belonging to the B-box zinc finger protein family in Arabidopsis thaliana, is involved in the regulation of thermotolerance. Using quantitative RT-PCR, GUS staining and immunoblot analysis, our results indicate that the expression of BBX18 was induced by HS. BBX18-RNAi and 35S::BBX18 transgenic Arabidopsis plants were obtained for functional analysis of BBX18. Under-expression of BBX18 displayed increased both basal and acquired thermotolerance in the transgenic plants, while over-expression of BBX18 reduced tolerance to HS in transgenic lines. Moreover, when wild-type, BBX18-RNAi and 35S::BBX18 transgenic plants were treated with HS, HR-related digalactosyldiacylglycerol synthase 1 (DGD1) was down-regulated by BBX18 in both normal and heat shock conditions. Besides, the expression levels of Hsp70, Hsp101 and APX2 were increased in BBX18-RNAi transgenic plants, but lower in 35S::BBX18 transgenic plants. However, the expression of HsfA2 was lower in BBX18-RNAi transgenic plants and higher in the 35S::BBX18 after high-temperature treatment. These results suggesting that, by modulated expression of a set of HS-responsive genes, BBX18 weakened tolerance to HS in Arabidopsis. So our data indicate that BBX18 plays a negative role in thermotolerance.