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It remains an open question whether violets use universal mechanisms, such as the production of metallothioneins, phytochelatins, and organic acids and/or rely on specific mechanisms like the production of antimicrobial cyclic peptides (cyclotides) for heavy metal tolerance. To contribute to the understanding of the role of cyclotides, we used seed-derived plants from metallicolous (M) and non-metallicolous (NM) populations of Viola tricolor, a pseudometallophyte tolerant to Zn and Pb. Eight- to ten-week-old plants were treated with 1000 mu M of Zn or Pb for 3 or 7 days and subsequently measured for cyclotides and heavy metal content using MALDI-MS and Atomic Absorption Spectrometry (AAS), respectively. Individuals from the M population accumulated a similar amount of Zn but occasionally more Pb in comparison with the NM population. Of the 18 different cyclotides included in the analysis, some showed statistically significant changes under the heavy metal treatment. In general, a decrease was observed in the M population, whereas an increase was observed in the NM population (except for the 3-day treatment with Zn). The day of treatment and dose of metal and their interaction played a crucial role in the explained variance for cyclotides produced by the M individuals but not for the NM plants. This unravels the importance of this antimicrobial compound in heavy metal tolerance and indicates that, in V. tricolor, cyclotides are involved in heavy metal tolerance, but specimens from two populations have developed different strategies and tolerance mechanisms involving cyclotides to mitigate heavy metal stress.