Physiological aspects of acidity stress in plants (synonymous with H+ rhizotoxicity or low-pH stress) have long been a focus of research, in particular with respect to acidic soils where aluminium and H+ rhizotoxicities often co-occur. However, toxic H+ and Al3+ elicit different response mechanisms in plants, and it is important to consider their effects separately. The primary aim of this review was to provide the current state of knowledge regarding the genetics of the specific reactions to low-pH stress in growing plants. A comparison of the results gleaned from quantitative trait loci analysis and global transcriptome profiling of plants in response to high proton concentrations revealed a two-stage genetic response: (i) in the short-term, proton pump H+-ATPases present the first barrier in root cells, allocating an excess of H+ into either the apoplast or vacuole; the ensuing defence signaling system involves auxin, salicylic acid, and methyl jasmonate, which subsequently initiate expression of STOP and DREB transcription factors as well as chaperone ROF; (2) the long-term response includes other genes, such as alternative oxidase and type II NAD(P) H dehydrogenase, which act to detoxify dangerous reactive oxygen species in mitochondria, and help plants better manage the stress. A range of transporter genes including those for nitrate (NTR1), malate (ALMT1), and heavy metals are often up-regulated by H+ rhizotoxicity. Expansins, cell-wall-related genes, the.-aminobutyric acid shunt and biochemical pH-stat genes also reflect changes in cell metabolism and biochemistry in acidic conditions. However, the genetics underlying the acidity stress response of plants is complicated and only fragmentally understood.