To identify transposons that may be of use for mutagenesis we investigated the genetic molecular basis of a case of flower colour variegation in Linaria, a close relative of the model species Antirrhinum majus. We show that this variegation is attributable to an unstable mutant allele of the gene encoding dihydroflavonol-4-reductase, one of the enzymes required for anthocyanin biosynthesis. This allele carries an insertion of a transposon belonging to the CACTA family (Tl1, Transposon Linaria 1) which blocks its expression thus conferring an ivory flower colour phenotype. Tl1 is occasionally excised in dividing epidermal cells to produce clonal patches of red tissue on the ivory background, and in cells giving rise to gametes to generate reversion alleles conferring a fully coloured phenotype. This finding may open the way for targeted transposon-mutagenesis in Linaria, and hence for using this genus in comparative genetic studies.