Homologous recombination is one of the major pathways for repairing DNA double strand breaks, the most deleterious of DNA lesions. Recent studies suggest that DNA methylation events target homologous recombination segments; however, the underlying mechanism of DNA methylation during homologous recombination is not understood. In this work, we show that GADD45α, a protein involved in cell cycle control, growth arrest, and apoptosis, plays some role in the epigenetic of homologous recombination. Specifically, it is suggested that dimerization of GADD45α monomers is required. Several point mutants of GADD45α were constructed and analyzed to show defects in self-association. Among them, the GADD45α mutant, CE83AA, lacked the ability to dimerize or oligomerize, which suppressed DNA methylation at homologous recombination sites in vivo. Based on this, we propose a model in which the dimerization (or oligomerization) of GADD45α is involved in strand specific DNA methylation that attends homologous recombination.