We previously reported spreading of RNA silencing that occurred from 5′ to 3′ direction along the transgene without any effect on transgene methylation by grafting transgenic Nicotiana benthamiana carrying either entire or 5′ region of coat protein gene (CP) of Sweet potato feathery mottle virus (SPFMV). Here, spreading of RNA silencing and transgene methylation was investigated in hybrids between these transgenic lines. When silenced line carrying 5′ region of CP was crossed with a non-silenced line harboring the entire CP, progeny showed very little accumulation of transgene mRNA and siRNAs were detected not only from 5′ region but also from middle and 3′ region of CP. This suggested that RNA silencing spread from 5′ to 3′ region over the entire CP transcript in hybrids. In addition, increased level of cytosine methylation in both symmetrical (CG and CNG) and asymmetrical (CHH) contexts (in the order of frequency, CG > CNG > CHH) were observed in entire transgene in hybrids. Together with the results, it is postulated that transitive silencing can induce spreading of transgene methylation depending on the system implemented reflecting the extent of interaction between silencing signal and transgene DNA in nuclei.