Genetically determined color morphs are found in many animals. Polymorphism can be maintained by social selection if competitive interactions allow each morph to increase in frequency when rare. This reliance on negative frequency-dependent selection should make color polymorphism vulnerable to the appearance of novel phenotypes that disrupt competitive interactions among morphs. We show that the origin and adaptive spread of a sexually selected syndrome in common wall lizards (Podarcis muralis) selectively eliminates alleles coding for alternative color morphs that have been maintained for millions of years. The results demonstrate how the arrival of a novel phenotype can disrupt balancing selection, providing a link between rapid phenotypic evolution and the loss of color polymorphisms.