Active transposition of the DNA transposon Ttf1 in the Torenia mutable line “Flecked” generates new mutants, including those with imperfect penetrance. However, when a gene responsible for a mutation is identified using the transposon display method, the high transposition activity of Ttf1 generates falsepositive bands, thus making identification difficult. In this study, we designed a transposon display method that uses the F₂ mutant-type population obtained from a cross between the mutant and another line harboring Ttf1 in a different genomic location. When this method was applied to the “Flecked” mutation, only the band containing TfMYB1, which is responsible for the mutation, was commonly detected in the mutant-type F₂ population, while the unspecific bands were segregated. Further, this method effectively identified the gene responsible for the “Petaloid” mutation, which displays imperfect penetrance. Thus, this method can be potentially used in various other crops to identify the mutations caused by highly active transposons, including those with imperfect penetrance.