The X-linked gene Hmr in Drosophila melanogaster, when mutated, rescues otherwise inviable interspecific hybrids from crosses between D. melanogaster and any of its three most closely related species D. simulans, D. mauritiana and D. sechellia. DNA from the site of a breakpoint at the putative locus of the gene has been cloned, and results of transcription and sequence analyses are presented. Three distinct mRNAs are transcribed from this locus, two of which are abundantly expressed throught life. A third transcript, which is larger but rarer, appears to be disrupted by at least one of the two known mutations of Hmr. The gene encodes a mitochondrial ADP/ATP translocator protein, which plays an essential role in maintaining metabolic energy. Analysis of several cDNAs suggested that the rescue of hybrids may be dependent on mutations in the variable 3′ end region of this gene, affecting the level and/or the stability of the largest messenger RNA.