For centuries, hybridization was a poorly understood process thought to be a threat to endangered species. With the advent of genomic technologies, those views are starting to change; hybridization is now recognized as vital for the formation and continued persistence of many species. However, our current system of protection under the Endangered Species Act (ESA) fails to take many of the modern nuances of evolutionary biology into consideration. Despite calls for an explicit “hybrid policy” since the early 1990s, the U.S. Fish and Wildlife Service and National Marine Fisheries Service have instead chosen to apply a case-by-case approach with no guidance or overarching policy. With the new technologies, many species we are currently protecting could technically be unsuitable for protection based on a rigid interpretation of the ESA. A defined hybrid policy must be adopted, taking into consideration the twin aims of protecting genetic lineages and protecting ecosystems.