Vertebrate pelvic reduction is a classic example of repeated evolution. Recurrent loss of pelvic appendages in sticklebacks has previously been linked to natural mutations in a pelvic enhancer that maps upstream of . The sequence of this upstream enhancer is not conserved to mammals, so we have surveyed a large region surrounding the mouse gene for other possible hind limb control sequences. Here we identify a new pelvic enhancer, , that maps downstream rather than upstream of drives expression in the posterior portion of the developing hind limb, and deleting the sequence from mice alters the size of several hind limb structures. sequences are broadly conserved from fish to mammals. A wild stickleback population lacking the pelvis has an insertion/deletion mutation that disrupts the structure and function of , suggesting that changes in this ancient enhancer contribute to evolutionary modification of pelvic appendages in nature.