The amount of boron in soil is important for agronomic plants. As an abiotic stress condition, boron toxicity causes significant decreases in crop yields. Puccinellia distans (Jacq.) Parl. (P. distans), common alkali grass, is found throughout the world and can survive in soils with boron concentrations that are lethal for other plant species. Indeed, P. distans accumulates very high levels of this element. Despite these interesting features, very little research has been performed to elucidate the boron tolerance mechanism in this species. In this study, P. distans samples were analyzed by RNA sequencing to identify genes and miRNAs related to boron tolerance and hyperaccumulation. The results indicated that the hyperaccumulation mechanism of P. distans involves many transcriptomic changes including: alterations in the malate pathway, changes in cell wall components that may allow sequestration of excess boron without toxic effects, and increased expression of at least one putative boron transporter and two putative aquaporins. MiRNAs are also altered under stress conditions. The presence of miRNAs as stress regulator elements is an example of post-transcriptional regulation of stress related mechanisms. Additionally these small RNAs could affect their target genes by positive or negative regulation. Therefore, changes not only in miRNAs but also in their targets are important to understand their roles in hyperaccumulation. For example, downregulation of miRNA under stress could cause target accumulation. These mechanisms could be key in plant adaptation to new conditions. Elucidation of the boron accumulation mechanism is important in developing approaches for bioremediation of boron contaminated soils.