Caenorhabditis elegans contains 50 to 150 collagen genes dispersed throughout its genome. We have determined the complete nucleotide sequences of two collagen genes, col-12 and col-13, that are separated by only 1800 bases and are transcribed in the same direction. The 951 nucleotides of their coding regions differ by only five nucleotides (99.5% identity). The amino acid sequences are identical except for two conservative amino acid changes within the putative secretory signal sequences, so the mature forms of the col-12 and col-13 collagens would be identical. The position and sequence of the intron (52 base-pairs) within the coding region of each gene are perfectly conserved. In contrast to the coding regions and the introns, the 5' and 3' flanking regions show little sequence similarity, col-12 and col-13 are expressed at similar levels at the same developmental stages, and appear to utilize conserved TATA boxes and transcription start sites. The major differences between the genes is that, preceding the initiator ATG, col-12 has a cis-spliced intron, while col-13 is transspliced. Thus, col-12 and col-13 are essentially identical in all aspects except that the col-12 mRNA has a 26-nucleotide cis-spliced leader at the same place where the col-13 mRNA has a 22-nucleotide trans-spliced leader. These results suggest that col-12 and col-13 are derived from a gene duplication and that sequence homology in the coding regions, but not in the flanking regions, has been maintained by gene conversion. The fact that the only significant difference between the two genes is in their modes of splicing suggests that cis and trans-splicing can be interchanged during gene evolution.