<p>As the second most cultivated crop group, legumes occupy vast cultivated areas and hold immense agricultural economic value. DNA methylation, a highly conserved epigenetic modification in legumes, is dynamically regulated by various methylation enzymes. In recent years, investigating the functional roles of DNA methylation in legumes has emerged as a pivotal research area, yet comprehensive reviews in this area remain limited. This review discusses <i>de novo</i> DNA methylation in plants, along with the dynamic mechanisms governing its maintenance, recognition, and removal, and further explores the applications of DNA methylation in legume domestication and improvement; its role in responses to biotic and abiotic stresses, and its impact on genomic stability and transcriptional regulation. Additionally, this review highlights the potential of DNA methylation in advancing legume breeding. By synthesizing current knowledge, this review provides valuable theoretical insights into the application of DNA methylation for legume improvement and genome optimization. It also offers valuable guidance for leveraging epigenetic modifications in legume breeding, improving nitrogen fixation efficiency, and regulating the expression of vital plant proteins.</p>