The examination of genetic stability is one of the most important issue in the evaluation of horticultural cryopreservation techniques. We have assessed random amplified polymorphic DNA (RAPD) markers by polymerase chain reaction (PCR) in a variety of cryopreserved plants. We previously found no or only small genetic differences between cryopreserved and mother plants, suggesting that the cryopreservation techniques were successful. In this study, we used long random primers for RAPD analysis of morphologically abnormal plants in order to evaluate the genetic variation in normal plants. We found that 7 out of 8 (88%) long random primers (20-base) amplified polymorphic bands from abnormal blueberries, the use of long random primers improved the effectiveness of the RAPD analysis compared with the use of 10-base primers. The long random primers amplified a total of 24 polymorphic bands, which distinguished 3 mutant blueberries from the tissue-culture plant and the successfully cryopreserved plants. Thus, we conclude that RAPD analysis with long random primers could be used to clearly identify genetic differences between morphologically abnormal plants after cryopreservation and normal plants.