The development of floral organs plays a vital role in plant reproduction. In our research, the () promoter-transgenic lines showed abnormal developmental phenotypes in stamens and petals. The aim of this study is to understand the molecular mechanisms of the morphological defects in transgenic plants. By performing transgenic analysis, it was found that the -promoted genes and the vector had no relation to the morphological defects. Then, we performed the expression analysis of the class A, B, and C genes. A dramatic reduction of transcript levels of class B genes ( and ) was observed. Additionally, we also analyzed the methylation of the promoters of class B genes and found that the promoter of was hypermethylated. Furthermore, combining mutations in , , and with the -silencing lines rescued the abnormal development of stamens and petals. The expression of was reactivated and the methylation level of promoter was also reduced in RdDM-defective -silencing lines. Our results showed that the RdDM pathway contributed to the transcriptional silencing in the transgenic -silencing lines. Moreover, the results revealed that fact that the exogenous fragment of a promoter could trigger the methylation of homologous endogenous sequences, which may be ubiquitous in transgenic plants.