The species-level designation of the Mexican softshell turtle, Apalone atra, has been repeatedly challenged, yet no DNA evidence has been collected. We conducted field studies of all the drainages of the Cuatro Ciénegas basin, and the only pure morphological population of A. atra found was in Tío Candido, the type locality for the species. One nuclear intron known to show species-level divergence in the family Trionychidae, 2 nuclear genes, and a mitochondrial gene revealed little molecular divergence for A. atra when compared with A. spinifera emoryi from the Rio Grande. Further, no reciprocal monophyly of the mitochondrial gene tree was seen between A. atra and A. s. emoryi morphotypes.