Transposable elements (TEs) are main components of eukaryote genomes-up to 50% in some vertebrates-which can replicate and jump to new locations. TEs contribute to shape genome evolution, actively by creating new genes (or exons) or altering gene expression as consequence of transposition, and passively by serving as illegitimate recombinational hotspots. Analysis of amphioxus TEs can help to shed light on the ancestral status of chordate TEs and to understand genome evolution in cephalochordates and early vertebrates. The Branchiostoma floridae genome project has revealed that TE content constitutes ∼28% of the amphioxus genome. Amphioxus TEs belong to more than 30 superfamilies, which represent a higher diversity than in vertebrates. Amphioxus TE families are also highly heterogeneous as generally none of their members are drastically more abundant than others, and none of the TEs seems to have suffered any massive expansion. Such diversity and heterogeneity make the amphioxus genome not to be particularly prone to major evolutionary changes mediated by TEs, and therefore favoring genomic evolutionary stasis. Comparison of TE diversity and content between amphioxus and vertebrates allows us to discuss whether or not a burst of TEs happened after the two rounds of whole-genome duplication that occurred during early vertebrate evolution.