Abstract Our previous work in Arabidopsis has demonstrated that the presence of acetic acid, a weak organic acid, induces the expression of ROF2, an FKBP immunophilin protein. FKBPs are peptidyl prolyl cis-trans isomerases (PPIase EC 5.1.2.8) that catalize the isomerization of peptidyl prolyl bonds between the cis and trans configuration. FKBP are ubiquitous proteins that can be found either as a single catalytic domain proteins or being part of more complex proteins. To assess the implication of FKBP proteins in weak acid tolerance in plants we have generated plant lines overexpressing Arabidopsis FKBP65 (ROF2). In presence of acetic acid, 35S::ROF2 grew better than wild type plants. On the other hand a rof1 rof2 mutant line showed weak organic acid sensitivity whereas the single rof1 and rof2 knock-out mutant have a similar behaviour than the wild type. Our results confirm that over-expression of ROF2 confers tolerance to intracellular acidification by increasing proton extrusion from cells. The phenotype can be explained by indirect activation of plasma membrane proton pump (H+-ATPase) because ROF2 activate K+ uptake and this causes depolarization of the plasma membrane and activation of the electrogenic pump. In absence of stress, in 35S::ROF2 transgenic plants we have observed floration delay, apical dominance and increased seed size. We have also found that 35S::ROF2 plants has an enhanced response to IAA. Furthermore the roots of rof1 rof2 mutants have a reduced number of lateral roots and exogenous application of IAA was able to revert this phenotype. Our hypothesis is that ROF2 is a positive regulator of either auxin biosynthesis or perception.