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Transposable elements (TEs) represent a major component of plant genomes and may provide the host genome with the necessary plasticity for its adaptative response. Polyploidy has played a major role in the evolution of plants (Wendel, 2000) and its success can be explained by the fact that a polyploid genome is not only the strict addition of the progenitor genomes, but that polyploidisation induces structural and functional modifications which represent important sources of novelty (Adams and Wendel, 2005). Our study aims at evaluating the implication of TEs in the genomic modifications that occur during the formation of a polyploid genome. Our plant model is oilseed rape (Brassica napus, AACC) originating from interspecific hybridization between B. rapa (AA) and B. oleracea (CC), and we dispose of newly synthesized B. napus allotetraploids resulting from independent AA x CC crosses. We developed sequence-specific amplification polymorphism (S-SAP) markers anchored in two different families of Brassica-specific TEs, an Athila-like retrotransposon and a MITE, which are contrasting TEs regarding their genomic organisation, dynamics of evolution, and mode of replication. Comparison of the S-SAP profiles and characterization of the polymorphism identified in the newly synthesized allotetraploids will provide new insights into the putative role of TEs during the creation of an allopolyploid species.