Human and sheep Melatonin receptor 1a (MTNR1A) gene information was used to clone a portion of the coding region of this gene in pigs, and to identify polymorphisms of the gene for its assignment to both the genetic linkage and physical maps. MTNR1A maps to pig chromosome 17, establishing a new region of conserved synteny between this chromosome and human chromosome 4. Furthermore, we have assigned MTNR1A to bovine chromosome 27 and sheep chromosome 26. The addition of genes like MTNR1A to livestock genome maps allows questions about evolutionary events and the genetic basis for quantitative traits in livestock to be addressed.