Post transcriptional gene regulation in wheat cultivars caused by boron (B) toxicity has not been reported to date. In this study, two wheat cultivars Bolal-2973 (B-tolerant) and Atay-85 (B-sensitive) were compared with regard to the transcriptional regulation of miR319, miR172 and miR398 and their plausible target genes in order to address differences in their performances under high B levels. The expression levels of Cu/ZnSOD gene were found to be greater in Atay exposed to toxic B compared to Bolal, as verified by stable expression level of miR398. In wheat cultivars, both toxic B concentrations might cause an induction of leaf senescence mechanism due to stable level of JA and ethylene-related miRNAs, miR172 and miR319. miR172 targeting transcription factor TOE1 was only induced under B toxicity in sensitive cultivar Atay. However, MY133 as target of miR319 was significantly upregulated under toxic B in both cultivars. Also, computational prediction of these miRNA targets in wheat was performed and their orthologs in Arabidopsis thaliana were determined. Functional protein association networks of proteins encoded by miRNA targets and gene ontology enrichment analyses of these genes were identified. We identified new sets of genes that are targets of miR172, miR319 and miR398 in T. aestivum. In addition, miR172, miR319 and miR398 are responsive to different nutrient deficiencies or toxicities such as Fe, P, B, S and Cu, suggesting crosstalk between the post-transcriptional regulatory mechanisms involving miRNAs in plants.