<p>Cryopreservation represents the most effective and convenient approach for the long-term storage of plant cells, tissues, and organs obtained or modified through biotechnological methods, including products of somatic hybridization. Here, we report the first successful cryopreservation of interspecific somatic hybrids between <i>Gentiana cruciata</i> L. and <i>G. tibetica</i> King ex Hook.f. using the encapsulation–vitrification technique with plant vitrification solution 3 (PVS3). The survival and recovery of plants following liquid nitrogen (LN₂) exposure were influenced by several factors, including the culture temperature of stock plants, the size of shoot tips, the duration of PVS3 incubation, and the media used before and after the cryopreservation procedure. The highest recovery rate (87.3%) was achieved from shoot tips smaller than 2&#xa0;mm, excised from plants grown at 21&#xa0;°C on medium without plant growth regulators (PGRs), and incubated in PVS3 for 3&#xa0;h prior to cryopreservation. Genetic stability of recovered plants was verified using flow cytometry, Start Codon Targeted (SCoT) polymorphism, and Inter-Simple Sequence Repeat (ISSR) markers. These results establish encapsulation–vitrification as a reliable strategy for conserving interspecific <i>Gentiana</i> hybrids and provide the first evidence that somatic hybrids can be successfully cryopreserved without detectable genetic variation.</p>