Complex biological processes require coordinated function of many genes. One evolutionary solution to the problem of coordinately expressing functionally related genes in bacteria and nematodes is organization of genes in operons. Surprisingly, eukaryotic operons are considered rare outside the nematode lineage. In Drosophila melanogaster, we found lounge lizard (llz), which encodes a degenerin/ENaC cation channel, cotranscribed with CheB42a, a nonhomologous gene of unknown function residing <100 bp upstream. These two genes were transcribed from a single promoter as one primary transcript and were processed posttranscriptionally to generate individual mRNAs. The mechanism did not involve alternative splicing, and it differed from the trans splicing used in nematode operons. Both genes were expressed in the same tissues, and previous work suggested that both may be involved in courtship behavior. A bioinformatic approach identified numerous additional loci as potential Drosophila operons. These data reveal eukaryotic operon-like transcription of functionally related genes in Drosophila. The results also suggest that operon-based transcription may be more common in eukaryotes than previously appreciated.degenerin/epithelial Na ϩ channel ͉ fruit fly ͉ ion channels ͉ lounge lizard ͉ CheB42a D egenerin/epithelial Na ϩ channel (DEG/ENaC) proteins form non-voltage-gated cation channels. Their functions vary widely and include mechanosensation, nociception (sensing acidic stimuli), salt sensing, and detecting the peptidergic neurotransmitter FMRFamide (1-4). During our investigation of Drosophila melanogaster DEG/ENaC channels, we discovered a genomic locus containing a DEG/ENaC gene, which we named lounge lizard (llz, CG33349), and a nonhomologous gene of unknown function (CheB42a) (5) that appeared to be transcribed in the same direction with a predicted intergenic distance of Ͻ100 bp. The close proximity of these two genes and the lack of obvious promoter sequences in front of the downstream gene suggested that they might be cotranscribed from a single upstream promoter. This organization would resemble that of the nematode operon, an elegant evolutionary solution for coexpressing genes that are part of the same biochemical pathway or physiological process (6, 7).Although abundant in nematodes, operons are thought to be rare in other eukaryotes. This is despite eukaryote's complicated cellular physiology and the intricacy of their genomes, which might predict that operon-like transcription would solve some of the problem of coordinately regulating genes (8). With this background, we hypothesized that the CheB42a/llz locus might be transcribed as a eukaryotic operon, and, hence, the two genes might be functionally related.