Boron is an industrially and biologically important element. However, the mechanisms of boron tolerance and its transport in bacteria and many other living systems are still not clearly understood. In this study, the boron resistance level of a boron-tolerant bacterium, Bacillus boroniphilus DSM 17376, was improved up to 300 mmol l(-1) boron, by employing an in vivo evolutionary engineering strategy based on batch selection under continuous exposure to gradually increasing boron stress levels. The resistance was heterogeneous within the final mutant population which ranged from about 1- to 16-fold of the wild type resistance at 150 mmol l(-1) boron stress level. Boron-resistant mutants had significant cross-resistance to iron and copper stresses, and were also cross-resistant to salt (NaCl) stress, suggesting a common resistance mechanism between these stress types. Additionally, highly boron-resistant mutants had up to 2.8-fold higher boron contents than the wild-type, when exposed to high levels of (150 mmol l(-1)) continuous boron stress throughout their cultivation. It was shown that evolutionary engineering is a successful approach to significantly increase bacterial boron resistance and investigate the complex mechanism of boron tolerance and transport in microbial systems.