Comparison of whole genome sequences of representative animals enables reconstruction of the ancestral bilaterian genome: the starting point from which most extant animal lineages evolved. The Hox gene cluster patterns the anterior–posterior axis of bilaterians. Here we show that this cluster was embedded within a larger homeobox gene cluster, the Super-Hox cluster, in the ancestral bilaterian. This Super-Hox cluster contained at least eight genes alongside the core Hox genes (‘EuHox’ genes).