The presence of extrachromosomal circular DNA (eccDNA) is associated with transposable element (TE) activity. However, both the epigenetic regulation of eccDNA and its impact on genome stability are poorly studied. I will illustrate how the study of eccDNA can illuminate genome dynamics. In Arabidopsis, using long reads, we sequenced the eccDNA compartment and the genome of Arabidopsis thaliana mutant plants affected in DNA methylation and post-transcriptional gene silencing. In these mutants, a high load of TE-derived eccDNAs with truncated and chimeric forms was associated with truncated and full-length TE neo-insertions in the genome. Additionally, we detected complex structural variations (SVs) notably at a disease resistance cluster, and several large tandem duplications specific of each mutant individual, suggesting that SVs have been overlooked in epigenetic mutants. We propose that a high load of eccDNA may alter DNA repair pathways triggering the accumulation of SVs. These observations could have implications in cancer cells where eccDNAs are abundant.