SCO proteins are copper-donor chaperones involved in the assembly of mitochondrial cytochrome c oxidase (COX). Mutations in the two human SCO-encoding genes, SCO1 and SCO2, produce tissue-specific COX deficiencies associated with distinct clinical phenotypes. Here, we report the identification and characterization of scox, the single Drosophila melanogaster SCO-encoding gene. Null mutations of the scox gene are associated with larval lethality, while mutations in its 5'UTR are associated with motor dysfunction and female sterile phenotypes. All mutant phenotypes may be rescued by a transgene encompassing wild-type scox. The analysis of the phenotypes associated with the D. melanogaster scox mutations shows that unimpaired COX assembly and activity is required for biological processes that specifically depend on an adequate energy supply. Finally, we identified the SCO1 orthologs in 39 eukaryotic species informative for a tentative reconstruction of the evolutionary history of the SCO function. Comparison of the exon/intron structure and other key features suggest that eukaryotic SCO genes descend from an intron-rich ancestral gene already present in the last common ancestor of lineages that diverged as early as metazoans and flowering plants.