Eukaryotic genomes are composed of features with known or putative functions such as genes, as well as highly variable amounts of repetitive entities such as transposable elements (TEs) and not annotated sequences dubbed genomic “dark matter". The origin of this anonymous DNA in plant genomes remains elusive though it is hypothesized that much could derive from TEs. Indeed, these genetic entities that are capable of duplicating in the host genome from one place to another have most seemingly been bombarding eukaryotic genomes for over a billion years, and the vast majority of this genetic material is not under selective constraints. As a result, TE copies accumulate mutations over time and this theoretically unlimited process eventually produces unrecognizable sequences aka genomic dark matter. In this work, we have developed approaches aiming at deepening the identification of repeated and repeat-derived elements in the Arabidopsis thaliana genome that resulted in the partial annotation of until then dark matter space. Our results therefore support the presence of an evolutionary continuum between repetitive elements and genomic dark matter in plants.