Rice is an economically important plant as well as a model organism. The rice genome consists of 35% retrotransposons. Although most of the retrotransposons are inactivated through evolutionary processes, they can be activated under various biotic and abiotic stress conditions. The main objective of this study was to explore the effects of herbicides on retrotransposon activities and the usage of retrotransposons in short-term mutagenicity tests. In this study, bentazone and an MCPA (2-methyl-4-chlorophenoxyacetic acid)-containing herbicide was used. Plant samples were grouped into three classes: control (untreated), 1% and 2% herbicide treatment. Retrotransposon activities were investigated by using the inter-retrotransposon amplified polymorphism (IRAP) marker technique. IRAP analyses were performed for Houba (Tos5/Osr13) retrotransposon. Polymorphism ratios were calculated with the Jaccard similarity index, and the significance of polymorphism was evaluated by one-way analysis of variance (ANOVA). We observed that the polymorphism ratios ranged from 8%-90% for Houba among plant samples. ANOVA showed that these variable ratios were statistically significant. Bentazone and the MCPA-containing herbicide increased the retrotransposon activities, and they might be responsible for DNA mutations. This study indicated valuable data for establishing retrotransposon-based short-term mutagenicity test in rice with suitable retrotransposons such as Houba.