DNA methylation changes were observed in all five studied introgression lines derived from a non-conventional F1 hybrid between rice and a perennial wild species Zizunia latifo1ia (Griseb.) Turcz. ex Stapf. The changes were found to be a general occurrence involving all types of analyzed DNA sequences, both random genomic DNA and known-function genes. The changed RFLP patterns due to DNA methylation changes were highly heritable among selfed generations. Our results may have implications for crop improvement by the introduction of alien genes via conventional sexual hybridization.