Allopolyploidy is known to have a significant impact on plant evolution, frequently causing epigenetic, structural and functional genomic modifications. Due to their transpositional activity and repetitive nature, transposable elements (TEs) may play a key role in these genomic alterations. We focused our investigations on one of the most recent Nicotiana allopolyploids (formed ca 0.5 MYA), i.e. N. tabacum (tobacco), which arose from hybridization between progenitors of the extant diploid species N. sylvestris and N. tomentosiformis, and which contains well characterized active TEs. We conducted TE annotations by using pipelines of the REPET suite on publicly available genomes. REPET analysis reveals that TEs represent over 65% of the three Nicotiana genomes, with a major contribution of retrotransposons (over 40%). Around 1900 to 2230 TE consensus sequences were generated for each genome, and clustered by the MCL algorithm. We analyzed the distribution and genome coverage of different active endogenous retrotransposon families - including Tnt1- across tobacco and its parental genomes. Preliminary results show that the distribution of clusters matching these families over the 3 Nicotiana species fits well with what is known about these retrotransposon biology, abundance and diversity. As shown for Tnt1, complete copies display a higher copy number and genome coverage than incomplete ones, underlying the persistent activity of this retrotransposon in these Nicotiana species. Such analysis could be adapted to infer the dynamics of other not fully characterized Nicotiana retrotransposon families.