DNA methylation is one of the most important epigenetic modifications playing crucial roles in diverse biological processes. Although DNA methylation has been intensively studied in mammals and plants, dynamic DNA methylation in molluscs has only just been understood. Here, we summarize the recent research progress on the wide variation of DNA methylation in different molluscs and tissues. Dynamic changes of methylation are also reported during mollusc growth and development as well as changes in response to environmental stresses. In molluscs, DNA methylation is quite diverse among species and occurs in the CpG and CpHpG (H = A, C or T) contexts of intragenic regions and repetitive elements. DNA methylation can be altered by different environmental stimuli, such as pathogens and abiotic stresses, and the alteration of DNA methylation in molluscs can influence the descendants with a constant selection pressure. DNA methylation can also cause long-lasting changes in the gene expression of neurons involved in long-term memory (LTM) storage. Different mollusc species have similar DNA methylation patterns, suggesting that DNMTs are essential for methylation establishment and maintenance in the molluscs genome. In summary, the characteristics of DNA methylation in molluscs are complex and indispensable part of the epigenome. In this review, we summarized the research achievement, which will pave the future path to complete understanding of mollusc DNA methylation.