Mineral imbalance in high-input agricultural ecosystems has become an acute concern in many developed countries. Relapse into low-input agricultural ecosystems, however, will cause mineral stresses to crops, resulting in reduced food productions. Under such natural soil conditions, some endemic plants can tolerate the mineral stresses because they have evolved to adapt to the stresses. Numerous studies have been conducted to clarify the chemistry of the mineral elements of interest in rhizosphere and to utilize the tolerant mechanisms in plants. In this chapter, the authors reviewed the research progress on molecular scale mechanisms of Fe-deficiency, Al-toxicity, and P-deficiency stresses in soils and their tolerances by plants. In low Fe-availability conditions, two Fe-acquisition mechanisms of plants have been clarified: enhanced Fe dissolution in rhizosphere by secreted proton/reductants/chelators followed by reduction of Fe3+ to Fe2+ and specific uptake of Fe2+ (Strategy I) and Fe dissolution by secreted hexadentate Fe3+-transporting molecule (phytosiderophore) by forming Fe3+-phytosiderophore complex followed by specific uptake of the complex (Strategy II). Two tolerant mechanisms against high Al-toxicity of soils have been reported: exclusion of Al from cytoplasm (exclusion mechanism) and detoxification of Al in plants (internal detoxification mechanism). Phosphorous acquisition mechanisms of plants from low P-availability soils would be (1) alteration of root architecture, (2) secretion of organic acids, (3) secretion of phosphatase, and (4) enhanced expression of P transporter on roots. Some of the molecular mechanisms for the expression of the tolerances and their application to the genetic improvement are also reviewed.