Homeobox genes from the urochordates Styela clava (AHox2) and S. plicata (AHox3) were cloned and analyzed. The two genes are homologous and Antennapedia-like. The homeobox regions have 87% identity at the nucleotide level and are identical at the amino-acid level. No introns are present in the homeobox region of AHox3, and AHox3 is represented at a low copy number per haploid genome. AHox2 and AHox3 represent the second type of homeobox gene found in this evolutionarily and developmentally important group of organisms.