Gene expression changes induced in response to developmental and environmental cues, as well as the maintenance and inheritance of these altered expression states, require epigenetic regulation. Epigenetic mechanisms comprise modifications at the chromatin level, including DNA methylation and alterations in nucleosome organization through the incorporation of specific histone variants and their post-translational modifications, as well as the involvement of various non-coding RNAs. Many of these processes and factors are evolutionarily conserved, while others are specific to photosynthetic organisms. This Special Issue is published in association with the EPIPLANT/SEB conference 2024 and the sessions dedicated to epigenetic plasticity and plant epigenetics at the SEB Prague 2024 conference, which brought together researchers working in model and crop species. It comprises reviews and original articles discussing insights into the epigenetic mechanisms in plants and other photosynthetic organisms, as well as avenues to improve their adaptability to the changing environment.