Mercury (Hg) is one of the most hazardous pollutants released by humans and is of global environmental concern. Mercury causes oxidative stress and strong cellular damages in plants, which can be attenuated by the biosynthesis of thiol-rich peptides (biothiols), which include glutathione (GSH) and phytochelatins (PCs). We analysed Hg tolerance and speciation in five Arabidopsis thaliana genotypes, the wild-type Col-0, three knockdown γ-glutamylcysteine synthetase (γECS) mutants and a knockout PC synthase (PCS) mutant. Mercury-PC complexes were detected in roots by HPLC-ESI-TOFMS, with its abundance being limited in γECS mutants. Analysis of Hg-biothiol complexes in the xylem sap revealed that HgPC2 occurs in wild-type Col-0 Arabidopsis, suggesting that Hg could be translocated associated with thiol-rich metabolites. Twenty genes involved in sulphur assimilation, GSH and PCs synthesis were differentially expressed in roots and shoots, implying a complex regulation, possibly involving post-translational mechanisms independent of GSH cellular levels. In summary, the present study describes the importance of biothiol metabolism and adequate GSH levels in Hg tolerance, and identifies for the first time Hg-PC complexes in the xylem sap. This finding supports that Hg-biothiol complexes could contribute to Hg mobilisation within plants.