Dicamba is one of herbicides used widely in agriculture today. The wide use of dicamba in agriculture represents a potential danger to the ecosystems and the environment. Thus, the present study is aimed to investigate the DNA damage levels and the DNA methylation changes in Phaseolus vulgaris subjected to whether dicamba and humic acids (HAs) have any protective effect on these changes. Randomly Amplified Polymorphic DNAs (RAPDs) and Coupled Restriction Enzyme Digestion-Random Amplification (CRED-RAs) were used to determinate the DNA damage levels and the changes in the pattern of DNA methylation. The results showed that dicamba (0.2, 0.4 and 0.6 ppm) caused RAPDs profile changes (DNA damage) as increasing, genomic template stability (GTS) as decreasing and DNA hypomethylation. However, these effects of dicamba seen at higher levels decreased after treatment with five different concentrations (2, 4, 6, 8 and10%) of HAs. The results of this experiment have clearly shown that HAs could be used effectively to protect bean seedlings from the destructive effects of dicamba.