Root growth of Arabidopsis thaliana is inhibited by proton rhizotoxicity in low ionic strength media when the pH of the medium is lower than 5.0. QTL analysis at pH 4.7 revealed that two major QTLs on chromosome 2 and 5 and an additional six epistatic interacting loci pairs control proton resistance in the Ler/Col recombinant inbred population. These genetic factors are independently associated with proton resistance in comparison to the known Al resistant QTL and epistases detected in the same RI population at 4 microM Al at pH 5.0. This indicates that different genetic factors regulate mechanisms of resistance to each stress in this plant species. No correlation was observed between proton resistance and Al resistance among 260 accessions indicating that there is no simple relationship between the genetic factors controlling each trait. Several accessions with different combinations of proton (pH 4.7) and Al (4 microM Al at pH 5.0) resistances were identified by phenotypic cluster analysis. Although this grouping was performed using root growth data, the degree of resistance was correlated with their sensitivity to short-term damage in the root tip, indicating that the same resistance mechanism controls proton resistance at different time scales. Resistant accessions grew better than sensitive ones in acid soil culture. This suggests that proton resistance in hydroponic conditions could be an important index in breeding programs to improve productivity in acid soil, at least in acid sensitive plant species.