A vitrification-based cryopreservation technique for storage of in vitro shoot tips of papaya has been tested to ensure applicability across a range of genotypes and to assess the stability of both genotype and phenotype of clonal material following cryopreservation. Shoot tips of twelve female genotypes were cryopreserved, regeneration percentages were determined and resultant plants were screened for genetic and epigenetic changes. Genomic DNA structure was studied using polymerase chain reaction (PCR) based randomly amplified DNA fingerprinting (RAF), and methylation patterns were monitored using the amplified DNA methylation polymorphism (AMP) PCR technique. Plantlets were regenerated following cryopreservation in all but one genotype and regeneration percentages of 61-73% were obtained from 6 genotypes. The regenerated plantlets showed varying levels of genomic DNA modifications (0-10.07%), and methylation modifications (0.52-6.62%) for detected markers. These findings have not been reported previously for papaya, and indicate some genotype dependent variability in DNA modifications occurred following cryopreservation which could result in somaclonal variation.