Multiple kinds of clones and restriction fragment polymorphisms are frequently encountered when analyzing genes of the tetraploid frog Xenopus laevis. Two types of cDNA clone have been isolated for homeobox gene 2. Analysis of their corresponding genomic clones confirmed the existence of clearly distinct restriction maps; in addition the nearby presence of two additional homeoboxes suggests that this region is homologous to the Hox 2 gene complex of mammals. We asked whether the genetic polymorphism in Xenopus results from increased allelic differences due to tetraploidy or from having duplicated Hox 2 complexes. Using X. laevis/Xenopus borealis interspecies hybrids we show that the two types of X. laevis homeobox gene 2 transcripts result from two different genetic loci. They cannot represent alleles of the same gene because they do not segregate independently in the F1 hybrid progeny. Most other X. laevis homeobox genes studied so far are also found in two versions. Thus X. laevis seems to have two homeobox genes, both of which are expressed, for each one present in mammals or other vertebrates.