Increased access to genome-wide data provides new opportunities for plant conservation. However, information on neutral genetic diversity in a small number of marker loci can still be valuable because genomic data are not available to most rare plant species. In the hope of bridging the gap between conservation science and practice, we outline how conservation practitioners can more efficiently employ population genetic information in plant conservation. We first review the current knowledge about the within-population genetic variation and among-population differentiation in neutral genetic variation (NGV) and adaptive genetic variation (AGV) in seed plants. We then introduce the estimates of among-population genetic differentiation in quantitative traits (Q_ST) and neutral markers (F_ST) to plant biology and summarize conservation applications derived from Q_ST–F_ST comparisons, particularly on how to capture most AGV and NGV on both in-situ and ex-situ programs. Based on a review of published studies, we found that, on average, two and four populations would be needed for woody perennials (n = 18) to capture 99% of neutral and adaptive genetic variation, respectively, whereas four populations would be needed in case of herbaceous perennials (n = 14). On average, Q_ST is about 3.6, 1.5, and 1.1 times greater than F_ST in woody plants, annuals, and herbaceous perennials, respectively. We suggest using maximum Q_ST rather than average Q_ST among trait comparisons. Hence, conservation and management policies or suggestions based solely on inference on F_ST could be misleading, particularly in woody species. We recommend conservation managers and practitioners consider this when formulating further conservation and restoration plans for plant species, and for woody species in particular.