Epigenetic reprogramming occurring during in vitro plant tissue culture processes is one of the fundamental determinants of somaclonal variation (SV) by altering the methylation dynamics of the plant genome. DNA methylation is regulated in CG, CHG, and CHH contexts via the MET1, CMT3, and DRM2/RdDM pathways and plays a critical role in gene expression, transposon silencing, and the maintenance of genome stability. Stress factors in the in vitro microenvironment (oxidative imbalance, continuous subculturing, plant growth regulators, and culture duration) trigger epigenetic instability. This process affects cellular reprogramming through transient or heritable methylation changes, which result in phenotypic deviations. Although these epigenetic alterations can lead to clonal fidelity problems in commercial micropropagation systems, they also provide a valuable source of variation for breeding programs. Monitoring DNA methylation dynamics can be achieved using rapid screening methods such as MSAP and metAFLP, in combination with high-resolution techniques such as bisulfite sequencing. Effective management of epigenetic stability through culture condition optimization, stress regulation, and epigenetic profiling holds strategic importance for controlled variation in plant biotechnology and breeding.