Recently, Lee et al. (2012, Science 335:966; 10.1126/science.1213506) demonstrated that mutation in either of the transmembrane protein encoding genes, TMEM138 or TMEM216 causes phenotypically indistinguishable ciliopathy. Furthermore, based on the observation that their orthologs are linked in a head-to-tail configuration in mammals and Anolis, but present on different scaffolds or chromosomes in Xenopus tropicalis and zebrafish, the authors concluded that the two genes were joined by chromosomal rearrangement at the evolutionary amphibian-to-reptile transition to form a functional module. We have sequenced these gene loci in a cartilaginous fish, the elephant shark, and found that the two genes together with a related gene (Tmem80) constitute a tandem cluster. This suggests that the two genes were already linked in the vertebrate ancestor and then rearranged independently in Xenopus and zebrafish. Analyses of the coelacanth and lamprey genomes support this hypothesis. Our study highlights the importance of basal vertebrates as critical reference genomes.