Plant viruses are important because of their threat to produce of crops products and also their application as research tools in molecular plant pathology and other fields in biotechnology is important. The most research and achivments in plant pathology depends on ability of plant's viral genomes to preserve, replicate and modify as infectious clones. The infectious clone is a full-length DNA clone in which infectious transcripts can be obtained in vitro or in vivo conditions with a suitable promoter. Infectious clones can be used to study the life cycle of viruses, replicate and express of viral genomes, understanding of virus-host interaction, functional genomics and germplasm screening as a part of pre-replication programs for virus resistance. However, the infectious clone of plant viruses may pose a risk to the environment due to its ability to return to the wild-type mode through recombination. This scientific review introduces the infectious clone in plant viruses and surveys the advantages and disadvantages of working with genetically modified plant viruses.