Transposable elements (TEs) are ubiquitous in the plant kingdom and can be a major component of plant genomes. TEs are DNA sequences that can change their position within genomes. Transposition of TEs can influence plant genes and genomes in many ways. TEs can restructure genomes through element-mediated chromosomal rearrangements and alter the genome size thus acting as agents of genome evolution. They also cause mutations by insertion into genes and affect the regulation of genes by inserting near promoters. There are some examples of mutations and other types of genetic variations associated with the activity of mobile elements and involved in flower development. The origin and extremely rapid diversification of flowering plants, which Darwin famously referred to as an “abominable mystery,” is one of the most extraordinary phenomena in evolutionary history. The most extensive manifestation of this morphological variability is found in the innumerable and surprising flower structures in plants adapted to the most contrasting environments. The wide floral diversification is a consequence of the arrangement of the organs (sepals, petals, stamens and carpels) in the four whorls of flowers and the shape that the various organs take, in particular the petal symmetry both in the individual flowers and in the organization of the inflorescences. This review will focus on how the activity of TEs has altered the activity of some genes controlling floral shape and inflorescence architecture in angiosperms.