The gut microbiota profoundly influences host epigenetics through microbial metabolites and enzyme regulation, shaping gene expression without altering DNA sequences. Key mechanisms include the biosynthesis of epigenetically relevant metabolites (e.g., SCFAs, amino acids, and vitamins), modulation of chromatin states, and regulation of DNA methylation and histone modifications. Dysbiosis can disrupt these processes, affecting metabolic and immune pathways. Studies highlight microbiota-driven epigenetic changes in immune function, metabolic homeostasis, and disease susceptibility. Additionally, microbial colonization dynamically alters histone acetylation and methylation, with dietary factors playing a crucial role. For instance, a Western-type diet reduces SCFAs availability, impairing histone modifications. Emerging evidence links microbiota composition to DNA methylation profiles, influencing cardiovascular and inflammatory gene expression. These findings underscore the microbiota’s role as an epigenetic regulator, revealing its potential impact on health and disease.