Three homeobox-containing genes from the nematode Caenorhabditis elegans are described. Two of them (
ceh-11 and
ceh-12) were isolated from a genomic library by hybridization at low stringency with the Ascaris lumbricoides homeobox AHB-1. The first clone contains a homeobox defining a new class of homeoboxes (
ceh-11). This gene maps on the third chromosome of C. elegans, at the same locus as
egl-5, a gene already known to be essential for the determination of specific neurons. In the second clone, sequence analysis revealed the existence of the third helix of a putative homeobox (
ceh-12) which is interrupted by an intron located upstream of the codon for the amino acid 45 of the homeodomain. Using the
ceh-11 homeobox as a probe, a third homeobox (
ceh-13) was isolated from a cDNA library. As
ceh-13 belongs to the labial class of homeoboxes, we conclude that, at the time when the nematode lineage diverged from the myriapod-insect and the vertebrate lineages, the duplication which led to the Antp and the labial families of homeoboxes had already taken place.