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Dynamic epigenetic changes during hibernation occur in some hibernating rodents, but these changes are poorly understood in hibernating bats. Populations of the greater horseshoe bat (Rhinolophus ferrumequinum) in north China hibernate and provide an opportunity to study how epigenetic markers and modifiers differ in the active and torpid states of a chiropteran. We used fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) and qRT-PCR techniques to determine changes in the global DNA methylation levels and mRNA expression levels of methylation-related proteins. These included DNA methyltransferase (DNMTs), methyl-CpG-binding proteins (MBPs, including MBDs, UHRFs, and zinc-finger protein family) in active and torpid R. ferrumequinum. In the torpid state, both the relative global methylation and the relative mRNA expression levels of some DNMTs and MBPs, including dnmt3b and zbtb4 , increased significantly compared to the expression levels of these in the active state. These changes may involve methylation or assist in regulation of a particular subset of genes according to hibernation status. This indicates that epigenetic mechanisms may exist and facilitate the hibernation process of R. ferrumequinum. [Display omitted] • The global DNA methylation level increased in torpid state. • Some MBPs showed higher mRNA expression levels in hibernation. • Epigenetic marker and modifiers may facilitate the hibernation of the great horseshoe bats. [ABSTRACT FROM AUTHOR]