While genetic diversity within species is influenced by both geographic distance and environmental gradients, it is unclear what other factors are likely to promote population genetic structure. Using a machine learning framework and georeferenced DNA sequences from >8,000 species, we demonstrate that geographic attributes of the species range, including total size, latitude, and elevation are the most important predictors of which species are likely to contain structured genetic variation. While latitude is well known as an important predictor of biodiversity, our work suggests that it also plays a key role in shaping diversity within species.