An estimated one-third of the globally threatened plant species have recalcitrant storage behavior, for which seed banking is relatively ineffective. Therefore, to understand seed storage behavior in Ivesia webberi, a threatened Great Basin Desert forb in the United States, we examined the effect of seed size and storage time on seed viability, evaluated inter-annual and inter-population variation in seed viability, and investigated the predictive accuracy of non-destructive seed viability testing methods (seed x-ray and multispectral imaging). The results showed a significant reduction in seed viability from three months to two years, suggesting that I. webberi seeds have recalcitrant storage behavior. Seed viability exhibited significant inter-annual, but not inter-population, variation across 11 I. webberi populations; seed size has no significant effect on seed viability. The x-ray and multispectral imaging methods had high classification accuracy (>80%) and could replace the widely used tetrazolium test, which destroys the seed germplasm, resulting in the cumulative reduction of stored seeds from periodic monitoring. This study demonstrates the utility of non-destructive methods for long-term seed viability monitoring, and shows that seed viability is not affected by population density which varies widely among the sampled I. webberi populations.