Abstract. Hybridization or the breakdown of reproductive barriers has perplexed conservationists for centuries. Hybridization between the golden-winged warbler (Vermivora chrysoptera) and blue-winged warbler (Vermivora cyanoptera) has received extensive study across North America for more than a century and indicates widespread, bi-directional genetic introgression. We found evidence fire is creating habitat conditions leading to isolation between nesting golden-winged warblers and blue-winged warblers. This effect is likely the result of fire's ability to promote grass cover and suppress woody plants, leading to habitat use partitioning between golden-winged warblers and blue-winged warblers. In addition to minimizing contact between the species, fire is creating habitat conditions on mixed sites that greatly favors golden-winged warblers over blue-winged warblers. Fire provides a plausible explanation for the original split in these sister species and its near elimination from eastern North America provides at least a partial explanation for the golden-winged warbler's extensive range-wide decline. Fire also provides a potential conservation tool by isolating golden-winged warbler and blue-winged warbler nesting populations. If nesting populations can be isolated, relatively rapid phenotypic sorting can be achieved, which could lead to a clearer distinction between the taxa as well as species preservation.