Viral agents that are obligate plant pathogens have different shapes and sizes and usually consist of nucleic acid and protein coat. They are different from other plant pathogens due to their unique structure. Viral genomes contain information necessary for replication of viruses and expression of their genes in plant. Many viral agents that cause disease in plants contain RNA as nucleic acid. Viral genome, which plays a direct role in the mechanism of disease in plants, plays an important role in evolutionary processes due to various external factors. It is known that genomes of viruses which cause problem on cultivated plants undergo genetic changes quite frequently. A variety of molecular biology techniques that are advancing day by day allow us to analyze and modify genomes on molecular level. Since genomes of plant viruses are small in size, they are suitable for researches on molecular level and great number of researches have been done in the last 50 years. Thus, it is possible to have better understanding of the organization of genomes. Understanding the genome structure of viruses offers an insight into their identification and development of control strategies.