Shortly after gene transfer technologies had been established for different plant species, the first reports emerged about transgenes showing unexpected segregation patterns due to unstable expression. Initially, the erratic expression behavior of transgenes was considered a nuisance that impeded the impact and efficiency of a new technology. With the investigation of transgene silencing effects, however, it soon became clear that transgenes had helped us in a rather unexpected way to identify novel molecular pathways that were highly relevant to plant development and evolution. This article gives an account of a journey that started with the analysis of transgene-related silencing events and that led to the discovery of a new molecular world of small RNAs and epigenetic marks that regulate plant gene expression and adaptation to environmental changes.