DNA methylation and histone modifications play important roles in genome function, including epigenetic gene regulation. These modifications undergo drastic changes when nuclei are reprogrammed during development and differentiation. Recent studies have enabled the detection of the dynamics of modifications in living cultured cells and mouse preimplantation embryos. DNA methylation was visualized using the methyl-CpG-binding domain of the human MBD1 protein. The level and distribution of histone modifications can be monitored by two different methods. One approach uses fluorescence/Förster resonance energy transfer (FRET)-based sensors and another uses fluorescently labeled antigen binding fragments of specific antibodies. These visualization techniques will facilitate future studies on epigenetic regulation related to development, differentiation, and disease.