We analyzed the variation patterns of DNA methylation in Arabidopsis thaliana seedlings after cryopreservation using methylation-sensitive amplified polymorphism. Of 662 fragments, 598 were shared by all the samples and their descendants; and among 64 different fragments, a varied 48 (75%) were genetically related to their descendants. Compared to the control, 14 sites showed de novo methylation, and 22 sites were demethylated in the samples after cryopreservation. Among samples treated with cryoprotection and after cryopreservation were 624 shared fragments and 38 fragments of difference, with 7.45% and 6.63% difference in the two treatment samples, respectively, as compared with the control. In conclusion, the results showed that whether cryostorage in liquid nitrogen or other treatments had impact on the DNA methylation states of the material in this study, and most of the change could be genetic to their descendants.