The dataset provides transposable elements annotation (cf Transposable_elements_Annotation) of 11 hexaploid wheat (ArinaLrFor, Jagger, Julius, Lancer, Landmark, Mace, Norin61, spelt wheat, Stanley, SY_Mattis, Zhang1817), 2 tetraploid wheat (Triticum dicoccoides, Triticum durum) and 2 diploid wheat (Triticum urartu, Aegilops tauschii). The annotation was conducted with the annotation tool ClariTE (GitHub - jdaron/CLARI-TE). The sequence used were downloaded from NCBI (https://www.ncbi.nlm.nih.gov/) for Zhang1817, Triticum dicoccoides, Triticum durum, Triticum urartu and Aegilops tauschii or from https://wheat.ipk-gatersleben.de/ for ArinaLrFor, Jagger, Julius, Lancer, Landmark, Mace, Norin61, spelt wheat, Stanley, SY_Mattis. The dataset provides also source files from orthology and sequence homology analysis (conducted with BLAST) of collinear intergenic regions between the wheat reference Chinese Spring and the other species/varieties (cf Conserved_Specific_Regions and Orthologous_Genes_Detection). Finally, the dataset provides informations about recent insertions of transposable elements detected in all the comparison analysed.