PCR primers derived from two functional domains of vertebrate carboxypeptidase E (CPE) were used to generate a probe for screening a size-selected Drosophila melanogaster genomic library. A sequence representing about 50% of the expected complete sequence was obtained by translation of the two open reading frames present on a 1.6 kb DNA genomic fragment. This partial sequence, homologous to human CPE, CPM, and CPN, contained the conserved arginine and zinc binding domains. Similarities to the human enzymes were found with stretches that were equally divergent from the three vertebrate carboxypeptidases. Northern blot analysis revealed the presence of a 6.9 kb transcript for this gene in Drosophila embryos. I postulate that insects possess a single protein fulfilling CPE, CPM, and CPN functions.