SummaryCG methylation (mCG) is essential for preserving genome stability in mammals, but this link remains obscure in plants. OsMET1‐2, a major rice DNA methyltransferase, plays critical roles in maintaining mCG in rice. Null mutation of OsMET1‐2 causes massive CG hypomethylation, rendering the mutant suitable to address the role of mCG in maintaining genome integrity in plants. Here, we analyzed mCG dynamics and genome stability in tissue cultures of OsMET1‐2 homozygous (−/−) and heterozygous (+/−) mutants, and isogenic wild‐type (WT). We found mCG levels in cultures of −/− were substantially lower than in those of WT and +/−, as expected. Unexpectedly, mCG levels in 1‐ and 3‐year cultures of −/− were 77.6% and 48.7% higher, respectively, than in shoot, from which the cultures were initiated, suggesting substantial regain of mCG in −/− cultures, which contrasts to the general trend of mCG loss in all WT plant tissue cultures hitherto studied. Transpositional burst of diverse transposable elements (TEs) occurred only in −/− cultures, although no elevation of genome‐wide mutation rate in the form of single nucleotide polymorphisms was detected. Altogether, our results establish an essential role of mCG in retaining TE immobility and hence genome stability in rice and likely in plants in general.