Basin wildrye (Leymus cinereus [Scribn. & Merr. Á. Löve]) is a perennial grass native to western regions of North America. Despite its importance for rangelands, stand establishment of basin wildrye is difficult due to its poor seedling vigor. We undertook to increase the seedling vigor of the basinwildrye cultivar “Trailhead” by using selection for emergence fromdeep seeding depth. We carried out two cycles of selection in two select populations and included two random populations, in which no direct selection occurred. We characterized the indirection effect of the selection on biomass, seed production, and stand percentage in these populations under field conditions. We used amplified fragment length polymorphic (AFLP)markers to identify regions of the genome associated with the selection by identifying allele frequency changes between the base population and the select and random populations. The second cycle select population and the first cycle random population possessed the highest total emergence from deep seeding (60% and 59%, respectively) compared with the base population (26%). The field evaluations showed no differences in genetic variation among the base, select, and random populations for biomass, seed production, and stand percentage. On the basis of the analysis of the AFLPmarkers, diversity increased slightly among the random populations and decreased slightly among the select populations. In the select populations, band frequencies increased for aggcac403, actcag185, and aggcac208. The band frequencies of aggctg212 and actctc66 decreased in both random and selected cycles. The results indicate that targeted selection for trait improvement in this native grass can be successfully completed with minimal effect on population genetic diversity.