In plants, RNA-directed DNA methylation (RdDM) is characterized by the production of 24-nt sRNAs from TE loci to guide the deposition of DNA methylation and the formation of heterochromatin. Duckweeds (lemnaceae) are a unique family of flowering plants characterized by evolutionary simplification of development and fast colonal asexual propagation. In contrast to Arabidopsis, duckweeds do not constitutively express RdDM and have lost some pathway components, resulting in the loss of 24nt sRNAs and associated DNA methylation. To understand TE regulation and genome stability during clonal reproduction, we investigated three species ranging from the most ancestral to the most evolutionary young. In duckweeds, TE silencing is maintained in the absence of somatic RdDM. However, the epigenetic landscape varies with the degree of TE colonization and age of TE insertions. In duckweeds with no recent TE activity, only few recent TE insertions are covered with DNA methylation and H3K9me2 silencing marks, while most TE sequences are associated with H3K9me1 and lack of DNA methylation. On the other side, species with more recent TE activity display higher levels of DNA methylation and H3K9me2 in all TE sequences. Finally, in recently derived species, where TE amplification has taken place in the very recent past, TE-derived 22-nt sRNAs, generally associated with PTGS, are very abundant. Hence, even in the absence of active RdDM, alternative sRNA pathways might contribute to the regulation of TE proliferation. Thus, duckweeds offer an interesting system to investigate unexplored mechanisms of TE silencing in plants and how TE-host dynamics shape epigenomes.