Yoga, an ancient practice rooted in Indian philosophy, has gained widespread popularity for its numerous physical and mental health benefits. In the recent years, there has been growing interest in understanding how yoga influences gene expression and epigenetic modifications. This narrative review investigates the molecular mechanisms, by which yoga influences gene expression, focusing on deoxyribonucleic acid (DNA) methylation, and histone modifications. Research literature was sourced from various databases to select randomized clinical trials and comparative cohort studies examining yoga's impact on gene expression and epigenetic changes. Our findings suggest that yoga could exert anti-inflammatory effects, as it downregulates pro-inflammatory cytokines, soluble interleukin IL-2 receptor gene expression, and transcription factors. Yoga also boosts the innate antiviral response and brain health by enhancing natural defense genes and microRNA-29c expression. Notably, it activates telomerase, linked with cellular longevity, and promotes nitric oxide synthetase and neuroprotective gene expression, implying benefits for ocular health. In addition, yoga fosters DNA repair and cellular integrity maintenance by increasing oxoguanine glycosylase one protein and p53 gene expression. However, the diversity of yoga interventions in these studies complicates direct comparisons and broader application. The current research primarily focuses on short-term outcomes, offering a limited understanding of yoga's long-term epigenetic impacts. Future research should address these gaps by studying the enduring effects of Yoga, personalizing interventions, and contrasting techniques.