Ancient, species-poor lineages persistently occur across the Tree of Life. These unique lineages are likely to contain unrecognized species diversity masked by the low rates of morphological evolution that characterize living fossils. Halecomorphi is a lineage of ray-finned fishes that diverged from its closest relatives over 200 million years ago and is represented by only one living species in eastern North America, the Bowfin Amia calva Linnaeus. We use double digest restriction-site associated DNA (ddRAD) sequencing and morphology to illuminate recent speciation in bowfins. Our results support the delimitation of a second living species of Amia with the timing of diversification dating to the Plio-Pleistocene. This delimitation expands the species diversity of an ancient lineage that is integral to studies of vertebrate genomics and development, yet is facing growing conservation threats driven by the caviar fishery.