Gene multi-functionization, by either duplication or co-option of new functions of an original gene, plays important roles in the evolution of animal complexities. Thus comparative analysis of orthologous genes in animals of sharply different complexities, like cephalochordates and vertebrates, can help us to understand the evolution of those complexities. Vertebrate Paxl and its paralog Pax9 derived from a common ancestral gene Pax 1/9 by gene duplication occurred after the divergence between cephalochordates and vertebrates. In vertebrates, Paxl is involved in the development of sclerotome and endodermal pharyngeal pouch. However, Pax 1/9 oi cephalochordate amphioxus is expressed only in the endoderm of the developing pharynx, and not in any mesodermal structures.