Oryza sativa (rice) has been extensively studied in genomics, but the effects of genotoxic stress on extrachromosomal circular DNA (eccDNA), a form of DNA located outside chromosomes from various sources, remain understudied. eccDNA, especially derived from transposable elements (TEs), may respond to stress conditions. Here we wanted to address if genotoxic stresses can induce changes in eccDNA biosynthesis in rice. We report on the results obtained with colchicine, a compound commonly used in plant breeding and known for disrupting microtubule formation during cell division, thereby inducing genome doubling. To determine its effects on eccDNA diversity in rice (var. Nipponbare) colchicine was applied to the culture medium at different concentrations (0.1% to 1%) after seed germination. Plant DNA was extracted at the maximum injury stage, and eccDNAs were amplified for mobilome sequencing. overall, we identified 2,428 loci, with some loci uniquely present in colchicine-treated samples and absent in controls, indicating distinct eccDNA diversity. Notably, down-regulated loci exceeded up-regulated loci in all treated conditions compared to controls. The types of down-regulated and up-regulated transposable element (TE) families varied. The Hopi TE family was significantly down-regulated across the 0.1% to 0.4% colchicine treatments compared to controls. Additionally, 85% of the up-regulated loci in the 0.9% treatment belonged to the Hopi TE family, which may be due to its high copy number. The Dasheng TE family exhibited a fourfold up-regulation in the 0.7% treatment but was down-regulated twofold in the 0.6% treatment compared to controls, indicating that eccDNA production is sensitive to colchicine dosage. No genes were detected as sources of eccDNA in the annotation. These findings suggest that colchicine concentration significantly affects eccDNA production and diversity and possibly TE mobility, offering insights into the interplay between genotoxicity and the mechanisms that maintain genomic stability in rice. This study highlights potential directions for future research into the effects of genotoxic substances on crop genomes.