1α,25-dihydroxyvitamin D 3 (1,25D 3 ) regulates many physiological processes in vertebrates by binding to the Vitamin D Receptor (VDR). Phylogenetic analysis indicates that jawless fishes are the most basal vertebrates exhibiting a VDR gene. To elucidate the mechanism driving VDR activation during evolution, we determined the crystal structure of the VDR ligand binding domain complex from the basal vertebrate Petromyzon marinus, sea lamprey (lVDR). Comparison of 3D crystal structure of lVDR-1,25D 3 complex with higher vertebrates VDR-1,25D 3 structures suggest that 1,25D 3 binds to lVDR similarly to human VDR (hVDR), but with unique features for lVDR around linker regions between H11 and H12 and between H9 and H10. These structural differences may contribute to the marked species differences in transcriptional responses. Further, residue co-evolution analysis among vertebrates VDR identifies amino-acid positions in H9 and the large insertion domain (iD) VDR LBD specific.