The variation of gene expression of seeds or leaves of Arabidopsis thaliana was investigated by irradiation with oxygen and air plasmas. The irradiation with oxygen plasma reported on the growth promotion and induced the consequence of gene expression in plant cells by neutral active oxygen species. The increase in leaf area ratio by oxygen plasma to seeds was due to epigenetics such as activation of DNA demethylation transcription factors and the growth enhancement effect induced by the plasma irradiation of seeds was inherited by next-generation cells through cell division even after germination. In oxygen irradiation for 10 s, expression of each de-DNA methylation-related gene increased, and DNA methylation-related genes decreased in expression. DNA acetylation that induces gene expressions was suppressed. However, irradiated for 20 s by oxygen, both demethylation suppression and promotion and methylation/acetylation suppression and promotion were obtained. On the other hand, methylation and demethylation may occur at the same time but were not significant and the acetylation was suppressed by air plasma irradiation. In both cases, active oxygen species was the key factor for the variation of gene expression.