In this study, we examined physiological, biochemical, and transcriptomic responses to toxic boron (B) treatment in leaves and roots of two wheat cultivars in order to gain better insight into B response or tolerance mechanisms. Delayed development and reduced vigor caused by high B were not observed in leaves and roots of both cultivars. Length, wet weight, and dry weight were not markedly changed under B toxicity. In leaves, when compared to control, 995 and 892 genes were significantly expressed at least twofold under B toxicity in Atay and Bolal, respectively. In roots, expressions of 1248 and 957 genes were responsive to B toxicity in Atay and Bolal, respectively. In leaf and root tissues, B toxicity induced more genes related to protein degradation in Atay than those in Bolal. These differences in transcriptome were attributed to higher B accumulation in the sensitive cultivar which required high level of metabolic adjustment. B toxicity stress did not cause any significant change in photosynthetic activity and contents of proline and glycine betaine in both cultivars. Coordinately, we did not find any differentially expressed genes required for proline and glycine betaine metabolisms. Genes related to hormone signaling, kinases, transcription factors such as WRKY and MYB, and key enzymes in reactive oxygen species (ROS) scavenging mechanisms were differentially affected by B toxicity in both cultivars. Among commonly regulated genes in Atay and Bolal, glutathione S-transferase (GST) and NIP4;1 (nodulin-26-like intrinsic proteins) genes stand out as prominent actors in B stress response.