Pandemics of viral diseases and significant epidemics pose a hazard to plants that provide food for people and animals, in addition to fiber or medicinal purposes. Among the food crops, fruit crops are the most susceptible to viruses that reduce yield and income for farmers. Epigenetic changes are required to transfer the stress-recovery memory to the next generations, as traditional breeding methods have failed to provide long-term remedies for the quickly spreading viral diseases. With respect to plant-pathogen interactions under unfavorable environmental conditions, epigenetic alterations are emerging as increasingly important regulatory mechanisms. Resistance to several diseases is conferred at the genetic level, preventing yield loss indefinitely. Transgenic and non-transgenic methods for creating virus-resistant crop plants have recently been made possible by RNA-based technologies, including CRISPR/Cas9, microRNA, and dsRNA- and siRNA-based RNA interference. Through epigenetic memory, the virus-infected plants can remember the previous molecular processes that enabled them to resist the virus, assisting in the achievement of sustained output, without altering the genome of the individual. When the condition recurs, they can use this knowledge to adjust and save lives. Through an explanation of several molecular breeding techniques and case studies, this chapter explores the different epigenetic mechanisms that provide resistance to fruit crops against viral diseases. Availability and high cost of the developing techniques also cause major problem for adapting these reliable and permanent solutions for improving resistance in fruit crops. A wide variety of fruit types and cultivars that may not be popular but are nonetheless nutritionally significant require more research. Integration of developing molecular breeding methods and epigenetic tools can offer virus-free fruit crops with sustainable yield and income.