The performance of crop plants is critically affected by biotic and abiotic stress. These stressors threaten food availability by reducing overall crop yield and productivity. Changes in chromatin state by epigenetic modification are part of plant adaptive and survival responses and are considered pivotal for improving agronomic traits. Epigenetics is an exciting field that involves heritable gene expression changes that do not require changes in DNA sequence. Epigenetic modification is well known as a crucial player in plant phenotypic diversity and defense against pathogens. Hence, there is a growing interest in unlocking the epigenome for crop improvement. Herein, we highlight the epigenetic modifications implicated in plant biotic stress response and their contributions to important agronomic traits. We also discussed adopting epigenetics to expand phenotypic diversity and produce desired characteristics in crop plants.