The origin of chordates and the consequent genesis of vertebrates were major events in natural history. The amphioxus (lancelet) is now recognised as the closest extant relative to the stem chordate and is the only living invertebrate that retains a vertebrate-like development and body plan through its lifespan, despite more than 500 million years of independent evolution from the stem vertebrate. The inspiring data coming from its recently sequenced genome confirms that amphioxus has a prototypical chordate genome with respect to gene content and structure, and even chromosomal organisation. Pushed by joint efforts of amphioxus researchers, amphioxus is now entering a new era, namely its maturation as a laboratory model, through the availability of a large amount of molecular data and the advent of experimental manipulation of the embryo. These two facts may well serve to illuminate the hidden secrets of the genetic changes that generated, among other vertebrates, ourselves.