Concerns over red wolf (Canis rufus) extinction caused by hybridization with coyotes (C. latrans) led to the capture and removal of remnant wild wolves from southwestern Louisiana and southeastern Texas, USA, during the 1970s. Here we show that despite decades of unmitigated hybridization, and declaration of endangered red wolves as functionally extinct in the wild, red wolf mitochondrial or nuclear DNA ancestry persists in ~55% of contemporary wild canids sampled in southwestern Louisiana. Surprisingly, one individual had 78–100% red wolf ancestry, which is within the range for 75% red wolf, red wolf backcross, or putative red wolf, depending on estimation method. Our findings bolster support for designation of red wolves as a distinct species, demonstrate a critical need for the United States Government to consider adopting an existing but unimplemented hybrid policy, and suggest that immediate reassessment of canid management and taxonomic designation in southwestern Louisiana may be warranted.