In plants, post-transcriptional RNA silencing (PTGS) signals move beyond their sites of synthesis using channels called plasmodesmata (PD). However, a potential influence of PD permeability in silencing signal movement has not been addressed previously. PD connectivity and aperture are routinely determined by monitoring the cell-to-cell movement of protein tracers of different sizes. Here we compare protein and RNA silencing signal movement during Arabidopsis embryogenesis. The data suggest that the degree of PTGS signal movement correlates with the degree of PD aperture previously determined in distinct subregions of the developing Arabidopsis embryo. Silencing signals move more extensively in the hypocotyl and root compared with the area around the tips of the cotyledons, suggesting that the site of silencing signal initiation influences the extent of signal movement. In addition, we found a putative boundary for silencing spread just below the shoot apical meristem that blocks movement upward from the root and hypocotyl. Finally, as PD aperture affects protein movement in embryos, we compared the movement patterns of protein tracers versus the movement patterns of RNA silencing signals. The data reveal that silencing signal complexes move to a similar extent as soluble proteins between 27–54 kDa.