Endoreplication is a process by which cells replicate their genomes without mitosis, resulting in an increase in nuclear DNA ploidy. This study is the first to report that oxidative stimuli from cryopreservation of seeds in liquid nitrogen induces endoreplication. We list evidence that the cryopreservation of red pitaya seeds (Hylocereus costaricensis) in liquid nitrogen for 30 and 60 days induced genome duplication stimuli via endoreplication. It was demonstrated that this conservation technique modulates the levels of hydrogen peroxide (H2O2) and antioxidant enzymes, triggering oxidative stimuli. The flow cytometry analysis of cladodes revealed different levels of ploidy between the tissues (mixoploidy) and that seedlings from the longest cryopreservation times of seeds showed higher percentages of octoploid nuclei when compared to the control treatment. The cryopreservation of seeds for 60 days also allowed increases of approximately 130% in seedling biomass, which is possibly related to the increases in ploidy levels resulting from endoreplication. It was also shown that cryopreservation of seeds with cryoprotectant solutions (PVS2) increases the efficiency of antioxidant metabolism in eliminating H2O2, repressing oxidative signalling and consequently endoreplication, maintaining ploidy levels and stable growth patterns. Oxidative signaling in seeds (induced by cryopreservation) triggers stimuli to promote endoreplication in pitaya seedlings, resulting increases in ploidy levels and in plant biomass.