A prevalent and persistent biodiversity concern is that modern cropping systems lead to an erosion in crop genetic diversity. Although certain trait uniformity provides advantages in crop management and marketing, farmers are also incentivized to use diverse genetics to reduce risks from change in climate, pests and markets. These risk factors have spurred increased turnover in varietal use to address complex and spatially variable genetics, environment, and crop management (GxExM) interactions to optimize crop performance. Contrary to commonly held perceptions, phylogenetically blind and phylogenetically informed diversity metrics reveal that the intensive use of scientifically selected varieties has led to significant increases in both the spatial and temporal diversity of the U.S. wheat crop over the past century.