Gossypium hirsutum and Gossypium barbadense are two allopolyploid species of cotton that have undergone two parallel domestication processes and represent the world's largest source of natural fiber. Recent research has provided good quality reference genomes of 8 and 11 different accessions of G.hirsutum and G. barbadense respectively, including both wild and domesticated populations. The current availability of such multiple high-quality reference genomes enables the development of reference pangenomes for genomic and evolutionary studies, which significantly improves the capture of the genetic diversity within a species in comparison to single reference genomes. With the aim of elucidating the roles of TEs in both the allopolyploidization and domestication events of these two species, we have analysed the LTR-RT content within the available G. hirsutum and G. barbadense genomes and its diploid parental species. Moreover, we have generated species-level pangenomes that allow us to study the more recent TE dynamics by looking into the structural variants triggered by TEs, also called TIPs (Transposon Insertion Polymorphisms). Our preliminary results reveal that different LTR-RT lineages show different dynamics after polyploidisation, with some lineages increasing their copy number accompanying the polyploidization event and others showing a relatively low activity and maintaining their copy numbers. Moreover, our results also show that the two tetraploid species seem to have undergone different LTR-RT recombination dynamics, evidenced by the presence of solo-LTR TIPs. These results illustrate how diverse the LTR-RT dynamics can be even within a single genome and how LTR-RT amplification and elimination by intra-element recombination shape a complex genome such as that of cotton.