Native prairie grasslands across the Northern Great Plains are critically imperiled due to land conversion and fragmentation. This poses a significant risk for many prairie plants, where reduced gene flow, isolation, and small population size may lead to loss of genetic diversity, reducing populations’ capacity to adapt to change. This is of particular concern for self-incompatible species, where reduced population size and isolation may increase the probability of mating between close relatives, thus increasing the potential for inbreeding depression. To evaluate the impact of fragmentation on the evolutionary potential of native prairie plant populations, we examined genetic diversity and connectivity across remnant prairie plant populations, using Helianthus maximiliani as a model species. We sampled 24 populations of this perennial, out-crossing, native prairie sunflower species from remnant prairie fragments across the Northern Great Plains. We used reduced-representation sequence data (RADseq) aligned to the Helianthus annuus reference genome to generate a SNP dataset of 6,206 genetic variants for a range of population genetics analyses. To assess population genomic structure, we looked at genetic clustering and pairwise genetic differences (FST) across populations and found evidence of genomic structure. We tested for the role of neutral and non-neutral processes in shaping the population’s genomic structure by evaluating the impact of geographic distance (i.e., IBD-Isolation by distance) and environment (i.e., IBE-Isolation by environment) on the evolution of genetic differences. However, neither IBD nor IBE was sufficient to explain the genetic differences among populations. We further estimated the long-term evolutionary potential across populations by estimating the effective population size (Ne) as a metric valuable to applied conservation management. Our analysis indicated that all populations exhibited extremely low effective population size (Ne < 2 00), suggesting that remnant populations may be increasingly susceptible to the consequences of genetic drift. Finally, we assessed population genetic structure and the distribution of genetic variation within and among populations. Using estimated effective migration surfaces (EEMS), we are identifying corridors of gene flow and potential areas to target conservation efforts to maintain connectivity and limit the fitness consequences of genetic erosion. Our results underscore the significance of maintaining connectivity across native prairie fragments and highlight the impact of anthropogenic changes on the evolutionary potential of native prairie plant populations.