Astragalus lentiginosus is the most taxonomically diverse species in the North American flora with over 40 named taxonomic varieties. However, these varieties are delineated somewhat arbitrarily and the number of varieties depends on the systematist. Thus, it remains unclear if varieties represent distinct population genetic entities. Many varieties are distinguished based upon variation in fruit morphology. The adaptive and functional significance of fruit morphological differentiation is unknown and it is possible that fruit variation is shaped largely by neutral genetic processes as populations of A. lentiginosus are often small and isolated. The goals of this study were to 1) characterize population genetic structure use ddRADseq among 16 taxonomic varieties from the southwest portion of distribution; and 2) to determine if fruit morphological variation exhibits a signature of being shaped by natural selection through a PST-FST analysis. Sequencing using ddRAD resulted in approximately 5000 SNPs for 400 plants that were collected from 79 sites among 16 taxonomic varieties. Population genetic analysis using STRUCTURE and PCA identified 3-4 major genetic groupings with significant isolation by distance and a single large genetic cluster in northern sites and 3 distinct clusters in the south. AMOVA revealed that a majority of the genetic variation occurred among varieties. Several taxonomic varieties represented unique genetic entities particularly narrow ranged taxa, whereas others exhibited considerable admixture and are not distinct. Morphometric geometric analysis of over 2,000 fruit images with a procrustes estimation of fruit shape was used to characterize fruit morphological variation. PST-FST analysis indicated that fruit morphological differentiation far exceeded underlying levels of population genetic differentiation suggesting that fruit morphological variation is likely adaptive. The selective force driving fruit morphological variation is uncertain. Fruits of A. lentiginosus are wind-dispersed and it is unlikely that wind dispersal generates spatially divergent natural selection across the landscape that might drive fruit adaptation. Defense against pre-dispersal seed predation by beetles is suspected to be shaping fruit morphological variation. Astragalus lentiginosus is an important study system given that many, but not all specimens, are toxic to grazing livestock, warranting the common name "locoweed". Additionally, several varieties are of conservation concern and receive some form of protective status.