Introduction. Physical exercise is one of the most powerful environmental factors modulating epigenetic modifications of the genome. The regulation of gene activity via the chemical modification of DNA, histone alterations, and non-coding RNAs serves as a link between training and the developing athletic phenotype. However, published data remain fragmented and often contradictory due to methodological challenges, heterogeneous cohorts, and a lack of protocol standardization. Objective. Systematization and synthesis of current data on the influence of physical exercise on epigenetic modifications of the genome, analysis of their contribution to the processes of adaptation, recovery, and formation of the risk of pathological conditions in athletes, as well as assessment of the prospects for the use of epigenetic markers in sports medicine. Discussion. Physical exercise induces specific changes in the three main components of the epigenome. Acute and chronic loads cause hypomethylation of the promoters of energy metabolism genes ( PPARGC1A , PDK4 , PPARD ), which is accompanied by increased expression and mitochondrial biogenesis. Histone modifications (acetylation, phosphorylation of H3.3-Ser-31, lactylation) alter chromatin packing density. The spectrum of microRNAs depends on the type and duration of training; however, information on individual microRNAs (including miR-1) remains contradictory, largely due to differences in methodology (participant training status, time points, normalization method, sex). Signaling cascades (AMPK, MAPK, IGF-1/Akt, NF-κB, NFE2L2) integrate energetic signals and the epigenetic response. The epigenetic response is tissue-specific and is modulated by sex, age, and ethnicity. Promising directions include the analysis of exerkines, including microRNAs from extracellular vesicles, and nutricepigenetics. Conclusions. Physical exercise consistently induces characteristic epigenetic modifications that participate in adaptation and can be considered as potential biomarkers of an athlete’s functional state. Promising areas of application in sports medicine include monitoring recovery through epigenetic clocks, predicting injury and overtraining, personalizing training, and extending the Athlete Biological Passport with epigenetic markers. Implementation of the results into clinical practice requires overcoming methodological limitations and further prospective research.