OBJECTIVES: To examine the effects of carbendazim on Arabidopsis genomic DNA methylation and gene expression. RESULTS: Carbendazim caused widespread changes in gene loci methylation and gene expression. With 0.1 mM (D2) and 0.2 mM (D3) carbendazim, there were, respectively, 1522 and 2278 demethylated sites and 1541 and 2790 methylated sites. A total of 279 and 505 genes were up-regulated by more than 300 % and 175 and 609 genes were down-regulated by 67 % in D2 and D3 treatments, respectively, compared with the control. Conjoint analysis showed that 20 and 39 demethylated genes were up-regulated >300 % and 21 and 24 methylated genes were down-regulated <67 % in D2 and D3, respectively. CONCLUSIONS: Carbendazim causes methylation or demethylation of certain genes and changes the expression of these genes. These findings provide a theoretical basis for novel epigenetics-based methods to detect organic food and a new interpretation for the degradation of crop varieties.