Using the even-skipped homeo box as a probe to identify diverged homeo box genes in the Drosophila genome, we isolated the empty spiracles (ems) gene. Structural and functional comparisons between ems and other embryonic patterning genes of Drosophila suggest that ems acts, in part, as a homeotic selector gene, specifying the identity of some of the most anterior head segments. Mutant embryos lacking ems protein have severe patterning defects in the anterior head and are missing tracheal structures, including the filzkörper, which are normally developed by the eighth abdominal segment. ems has two different spatial patterns of expression during embryogenesis. The early, head-specific pattern consists of a single anterior stripe at the syncytial and cellular blastoderm stages. The later, metameric pattern consists of bilateral patches of ems expression in neural and ectodermal cells of every head and body segment. Variations of the ems expression pattern in bicoid mutants suggests that the morphogen protein produced by bicoid has a concentration-dependent regulatory role in the establishment of head-specific ems expression. In contrast, the metameric ems pattern is initiated independently of bicoid protein, and ems becomes expressed at high levels in the primordia of the duplicated fïlzkörper that develop in the anterior half of bicoid mutant embryos.