Background:Transposable elements (TEs) are mobile pieces of genetic information with high mutagenic potentialfor the host genome. Transposition is often neutral or deleterious but may also generate potentially adaptivegenetic variation. This additional source of variation could be especially relevant in non-recombining speciesreproducing asexually. However, evidence is lacking to determine the relevance of TEs in plant asexual genomeevolution and their associated effects. Here, we characterize the repetitive fraction of the genome of the commondandelion,Taraxacum officinaleand compare it between five accessions from the same apomictic lineage. The mainobjective of this study is to evaluate the extent of within-lineage divergence attributed to TE content and activity.We examined the repetitive genomic contribution, diversity, transcription and methylation changes to characterizeaccession-specific TEs.Results:Using low-coverage genomic sequencing, we report a highly heterogeneous TE compartment in the triploidapomictT. officinalerepresenting up to 38.6 % of the homoploid genome. The repetitive compartment is dominated byLTR retrotransposon families accompanied by few non-LTR retrotransposons and DNA transposons. Up to half of therepeat clusters are biased towards very high read identity, indicating recent and potentially ongoing activity of these TEfamilies. Interestingly, the five accessions are divided into two main clades based on their TE composition. Clade 2 is moredynamic than clade 1 with higher abundance ofGypsy Chromovirussequences and transposons. Furthermore, a few low-abundant genomic TE clusters exhibit high level of transcription in two of the accessions analysed. Using reducedrepresentation bisulfite sequencing, we detected 18.9 % of loci differentially methylated, of which 25.4 and 40.7 % areannotated as TEs or functional genes, respectively. Additionally, we show clear evidence for accession-specific TE familiesthat are differentially transcribed and differentially methylated within the apomictic lineage, including oneCopia Ale IILTRelement and aPIF-HarbingerDNA transposon.Conclusion:We report here a very young and dynamic repetitivecompartment that enhances divergence within oneasexual lineage ofT. officinale. We speculate that accession-specific TE families that are both transcriptionally andepigenetically variable are more prone to trigger changes inexpression on nearby coding sequences. These findingsemphasize the potential of TE-induced mutations on functional genes during asexual genome evolution.