MicroRNAs (miRNAs) are 20-22nt long non-coding RNAs involved in the regulation of many important developmental and environmental response pathways in plants and animals. Regulation is achieved by recognition of target mRNAs by the miRNA leading to repression of expression. In plants, efficient gene silencing requires high complementarity between the miRNA and its target mRNA binding site. However, not all mRNAs with sequences highly complementary to the miRNA are efficiently silenced. This suggests high binding site complementarity alone does not ensure gene silencing. Rather, factors beyond binding site complementarity are involved in miRNA-mediated gene silencing. Previously, our lab has studied a target mRNA, MYB33, in Arabidopsis thaliana and found conserved sequences proximal to the miRNA binding site to impact the silencing of this gene. These conserved sequences are predicted to form a RNA secondary structure. Introducing mutations to destroy and subsequently restore this structure abolishes and restores silencing, respectively, thus implicating the role of RNA secondary structure in miRNA-mediated gene silencing. Along these lines, I demonstrate that the silencing of other target mRNA also require factors beyond binding site complementarity. Here, I have found other canonical target mRNA to possess conserved sequences proximal to the binding site, some of which are also predicted to form conserved secondary structures. I also demonstrate, using stable transformants, that mutations to these conserved sequences perturbs silencing of these genes. These findings suggest that the involvement of factors beyond binding site complementarity in the silencing of target mRNA is a widespread phenomenon. Further understanding of these factors and their mechanism in miRNA-mediated silencing has downstream implication for biotechnological tools, such as target mRNA prediction tools, and RNAi and miRNA decoy technology.