Different mechanisms regulate expression of several host endogenous genes in plants and this mechanisms interfere with the transcription and replication of virus infection. In addition, gene silencing, limits the level of viral replication in plants, and reduces symptoms of viral infection in host plant. Tomato leaf curl virus (ToLCV) belongs to family Geminiviridae which in combination with DNA beta satellite causes severe loss in tomato. DNA beta satellite encodes a protein, named βC1 that has a role in the symptoms, pathogenicity and suppression of gene silencing. In this study, effect of DNA beta satellite on the expression of several DNA methylation related genes in Tomato leaf curl virus (ToLCV) and beta satellite infected plants. Tomato plants were agro-inoculated at four-leaf stage with infectious clones of Tomato leaf curl virus (ToLCV) and DNA beta satellite were investigated. After 21 days, total DNA was extracted based on cTAB method. The presence of Tomato leaf curl virus (ToLCV) and beta satellite was approved by Polymerase chain reaction (PCR) , then total RNA was extracted from the leaf tissues by RNX – plus kit. Then RNAs were subjected to complementary DNA (cDNA) synthesize by Oligo dT primer. Expression of methylation related genes including argonaute4 (AGO4) and Adenosine kinase (ADK) was tested by real-time quantitative PCR. Results indicated that the expression of some genes including argonaute4 (AGO4) and Adenosine kinase (ADK) have been changed when tomato infected by DNA β satellite. The main role for this genes are khown as an important factor in gene silencing.