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Plants that inhabit Antarctica have raised scientific interest due to their resilience to climate change, abiotic tolerance mechanisms and potential biological applications. In vitro propagation is useful for conservation, genetic material availability of these species and avoiding mass collection in their habitat. In vitro culture protocols for the native plants Colobanthus quitensis and Deschampsia antarctica and the non-native Juncus bufonius have been affected by endophytic microorganisms that proliferate when introduced to tissue cultures. This study evaluated the microbicidal and phytotoxic effect of calcium hypochlorite (Ca(ClO) 2 ), silver nitrate (AgNO 3 ) and silver nanoparticles (AgNPs), and their use at different concentrations for different time periods. The Ca(ClO) 2 at 100 mg mL -1 showed the best microbial contamination control in D. antarctica (applied for 20 min) and for the three C. quitensis populations (applied for 15 min). In J. bufonius, AgNO 3 at 10 mg mL -1 for 10 min reduced the microbial growth, but oxidative damage was generated. AgNPs did not prevent contamination or have adverse effects on tissues. Survival plantlets from each treatment, population or species were effectively introduced to the tissue culture and their propagation was successful. These results constitute a fundamental advance for the introduction, propagation and conservation of Antarctic species and their use in scientific research.