Transposon display (TD) is a modification of the AFLP technique that uses a primer anchored in a transposon to simultaneously detect up to several hundred markers in the genome. TD involves the amplification of sequences flanking the transposon by ligation-mediated PCR, so the resulting fragments are locus-specific and can be analyzed by polyacrylamide gel electrophoresis. TD has been used to study the behavior and stability of transposable elements, including retrotransposons, in various organisms (Flavell et al., 1998; Van den Broeck et al., 1998; Waugh et al., 1997; Purugganan and Wessler 1995). Thus, both DNA and RNA transposons can be utilized in TD to generate molecular markers. Current marker technologies have their own advantages and disadvantages. RFLPs are reproducible but difficult to perform and/or yield a low density of markers. RAPDs are straightforward but lack reproducibility. AFLPs yield a high number of markers but they tend to cluster in heterochromatin regions. SSRs are likewise straightforward but require prior sequence information. TD has several potential advantages over these technologies when coupled with a particular class of transposable elements known as MITEs.