In an attempt to functionally characterize a petunia zinc-finger gene ZPT2-10, which is specifically expressed in style transmitting tissue, we fused its cDNA downstream of the potato SK2 promoter (SK2:ZPT2-10) and then introduced it into Petunia hybrida. We found that some transformants had acquired altered traits in compatibility in mating; these were termed ‘transgene-dependent incompatibility (TDI)’. These transgenic lines were fertile when self-pollinated or crossed with other TDI lines. In contrast, they failed to mate when crossed with untransformed wild-type petunia or non-TDI lines of SK2:ZPT2-10 transformants. The TDI phenomenon was observed irrespective of whether the TDI lines were used as the pollen or pistillar parent. The TDI phenotype cosegregated with the SK2:ZPT2-10 transgene in the T1 generation and loss of this transgene resulted in the recovery of normal fertility. In the case of infertile pollination with the TDI line as one parent, pollen tubes grew normally through pistillar tissues, where endogenous ZPT2-10 is expressed, and eventually reached the ovules. However, the resultant embryos were arrested at the globular-heart stage. We found no correlation between the occurrence of the TDI phenotype and the expression of ZPT2-10 transcripts. On the basis of these observations, we discuss the possible molecular mechanisms underlying this phenomena and its utility.