In recent years, transposon insertion polymorphisms have been utilized as molecular markers, and a range of techniques tailored towards identification of insertion sites of various transposable elements have been developed. In the present paper we describe the application of a recently developed DcMaster transposon display system to analyse the genetic diversity of Polish breeding materials of carrot (Daucus carota) and to identify polymorphisms useful for hybrid seed purity testing. Using 3 sets of breeding materials (each consisting of the cytoplasmic male sterility stock, the maintainer, the pollinator, and the corresponding F1 hybrid), we identified 56 DcMTD markers. DcMaster insertion sites proved to be highly polymorphic in cultivated carrot, as 79% of all insertion sites differentiated between individual plants. Fourteen stock-specific DcMTD markers were further selected as potentially useful for hybrid seed purity testing.