The receptor tyrosine kinase type III subfamily includes the PDGF receptors (alpha and beta), c-kit and the colony stimulating factor 1 receptor (CSF1R). The similar genomic organization of the genes encoding these receptors and the observation that in mammals, the genes for PDGFR alpha and PDGFR beta are tandemly linked with the c-kit and CSF1R genes, respectively, suggest that these genes arose from an ancestral receptor tyrosine kinase gene. We have previously cloned two copies each of the PDGFR beta and CSF1R genes from the pufferfish, Fugu rubripes, and shown that they are tandemly linked. We have now cloned the Fugu PDGFR alpha and c-kit genes and show that they are also tandemly linked. The intergenic region between the two genes in the Fugu (13 kb) and humans (350 kb) contains a conserved 59 bp element, which may play a role in regulation. The Fugu PDGFR alpha gene is transcribed from two promoters giving rise to alternate transcripts.