Epigenetics refers to the heritable changes in gene expression without any alteration in DNA sequence, including DNA methylation, histone modification and chromatin conformation. Epigenomics deals with global analyses of epigenetic changes across the entire genome. In the fields of epigenetics and epigenomics, DNA methylation has been drawn a special attention because of its close correlation to human development and carcinogenesis. In recent years, a variety of methods have been developed to study DNA methylation and other epigenetic modification. This review introduces and compares the new methods for epigenomics study and provides useful information for the researcher in this area.