polyhomeotic (ph) is a complex locus in Drosophila defined by two genetic units. Two mutational events are necessary to obtain the null lethal phenotype. Molecular analysis has shown that the ph locus contains two transcriptional units coding for two very similar proteins. Although a strong argument in favor of a strict correlation between the genetic and molecular units can be constructed, there is no direct evidence for the hypothesis. Here, we show for all cases with detectable molecular defects that X-ray-induced generation of an amorphic allele from a pre-existing X-ray-induced hypomorphic allele with a lesion limited to one unit invariably involves a rearrangement in the other unit. This result proves that each genetic unit corresponds to one transcription unit.