Ex situ plants` long-term conservation can be accomplished through cryopreservation procedures applied on meristems or somatic embryos. To achieve long-term preservation in the rare endangered species Dianthus nardiformis Janka, embryogenic aggregates, maintained for five years in slow growth culture were used for cryopreservation applying an encapsulation-dehydration protocol. Further, regenerants derived from slow growth culture and those recovered after cryopreservation were evaluated using allozymes and ISSR markers. A successful protocol for cryopreservation of synthetic seeds was obtained, being validated by a high reco­very rate (79.1%) after cryopreservation. The rate of polymorphism detected in the clones regenerated from cryopreserved synthetic seeds was lower (20.2%) compared with clones derived from slow growth cultures (30.8%). The isoenzyme and ISSR patterns showed changes which did not appear to be associated with the cryopreservation, but rather being related to the slow growth culture maintenance during long period.