In the free-living model nematode, Caenorhabditis elegans, a protein-folding co-transcribed gene pair has previously been described. The degree and form of trans-splicing, orientation and spacing of the genes, and the co-ordinate co-expression of protein folding catalysts in the nematode's hypodermis indicated this to be a functionally important operon. This gene pair has now been cloned and compared in the related organism Caenorhabditis briggsae to identify evolutionarily conserved, functionally important features. The corresponding C. briggsae gene pair was found to share the operon-specific features, including sequence homology blocks in the upstream 5' flanking regions. The intergenic regions were not conserved. The homology block closest to the translational initiation codon of the upstream gene was found to contain a known Ceanorhabbitis promoter element site, and may therefore be an important cis-regulatory region directing the hypodermis-specific expression of this operon gene of C. elegans. This study also provides further confirmation of the high degree of chromosomal synteny between these nematode species.