DNA methylation is one of the most important modifications in epigenetics, and becomes increasingly popular in ecology. Based on published papers about ecological epigenetics, principle, advantages and limitations, applications and prospects in ecology are discussed. Methylation-sensitive amplified polymorphism (MSAP) has been an effective method for DNA methylation because of its wide range of applications and simple operation, especially on subject of ecology problems, such as rapid adaptation to changing habitats and overcoming genetic bottleneck for alien invasive species. MSAP can reveal epigenetic variation within or between populations well, and acts as apowerful supplement to the study of genetic diversity and variation.