Unicellular green algae are a diverse and ecologically crucial group, serving as primary producers in a wide range of aquatic ecosystems and producing valuable biomolecules in human hands, thanks to their remarkable phenotypic and metabolic plasticity. Among the different regulatory mechanisms explaining these capacities, epigenetics plays a key role. This review focuses on the epigenetic regulation of the model species Chlamydomonas reinhardtii, focusing on the role of DNA methylation [C5-methylcytosine (5mC), N6-methyladenine (6mA)], histone post-translational modifications (PTMs), and noncoding RNAs (ncRNAs) in modulating gene expression, maintaining genome stability, and enabling acclimation to several environments. This review also explores the evolutionary significance of these marks and the potential role of the unique epigenetic patterns in this species.