In vertebrates, Hox genes play a key role in specifying positional identity along the anteroposterior axis. However, little is known about the function of these conserved genes in invertebrates other than in insects and nematodes. Now, surprisingly, Hidetoshi Saiga and colleagues report that Hox genes have limited functions during the larval development of the protochordate Ciona intestinalis (see p. 1505). In C. intestinalis, seven Hox genes are expressed during embryogenesis. Using antisense morpholino oligonucleotides directed against each of these genes, the researchers show that Ci-Hox12 plays an important role in tail development by maintaining the expression of Ci-Fgf8/17/18 and Ci-Wnt5 in the tail tip epidermis, and that Ci-Hox10 is involved in the development of GABAergic neurons in the dorsal visceral ganglion. Unexpectedly, however, knockdown of Ci-Hox1, 2, 3, 4 or 5 causes no consistent morphological defects. Thus, the contribution of Hox genes to the patterning of the larval anteroposterior axis in C. intestinalis might be very limited, a result that challenges the accepted paradigm for Hox gene function.