Technical Abstract: Questions often arise concerning the genetic stability of plant materials stored in liquid nitrogen for long time periods. This study followed the genetic stability of cryopreserved shoot tips of Rubus germplasm that were stored in liquid nitrogen for over 12 years, then rewarmed and regrown. We analyzed the genetic stability of R. grabowskii, two blackberry cultivars (‘Hillemeyer’ and ‘Silvan’) and one raspberry cultivar (‘Mandarin’) after regrowth in vitro, transplanting to the greenhouse and transfer to the field. No phenotypic differences were observed in greenhouse-grown cryopreserved plants when compared to the control mother plants. In the field, cryopreserved plants were more vigorous than mother plants as is common for plants derived in vitro. SSR and AFLP analyses were performed on shoots immediately after recovery from cryopreservation and on shoots subcultured for seven months before analysis. No SSR polymorphisms were observed between cryopreserved shoots and the corresponding mother plants irrespective of subculture. AFLP revealed polymorphisms in three of the four Rubus genotypes subcultured for seven months while no polymorphism was detected in those analyzed immediately after recovery from cryopreservation. Greenhouse and field-grown plants from the polymorphic shoot tips of R. grabowskii and ‘Silvan’ displayed the same AFLP fingerprints as their corresponding mother plants. Only long-cultured in vitro shoot tips displayed polymorphisms and they were no longer detected when the plants were grown ex vitro. The transitory nature of these polymorphisms should be carefully considered when monitoring for genetic stability.