The synteny conservation of the members of eukaryotic operons was investigated by mapping their orthologues in Drosophila, human, and other eukaryotes. While the homologues of the operon members are generally not linked, some examples of highly conserved syntenies were found. The most significant synteny involves two members of one C. elegans operon, encoding fibrillarin and ribosomal protein S16. Their homologues are linked in human, mouse, Drosophila, Anopheles gambiae, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Plasmodium falciparum, and Guillardia theta, but not in five other genomes. The distances between the genes are larger than in the nematode, suggesting the prevalence of intrachromosomal rearrangements.