The Hoxa-2 gene was disrupted by homologous recombination. Homozygous mutant mice died at birth. Defects were found in the branchial region of the head, which corresponds to the Hoxa-2 rostral expression domain. While rhombomeric and neural crest cell (NCC) segmentation was not affected, mesenchymal NCC derivatives of the second arch were lacking, and second arch mesenchymal NCC identity was changed to first arch identity, resulting in homeotic transformation of second to first arch skeletal elements. These results reveal the existence of a skeletogenic ground pattern program common to at least the mesenchymal NCC that originated from rhombomeres 2 and 4. The appearance of an atavistic reptilian pterygoquadrate element in Hoxa-2 mutants suggests that this ground pattern is intermediate between reptiles and mammals. The ground pattern program appears to be modified in the mouse first arch by a Hox-independent process, whereas Hoxa-2 acts as a selector gene in the second arch.