Hemlock woolly adelgid (Adelges tsugae Annand) (HWA) is an invasive forest insect sweeping across the native range of eastern (Tsuga canadensis [L.] Carr.) and Carolina (Tsuga caroliniana Engelm.) hemlocks, threatening to severely reduce eastern hemlock extent and to push Carolina hemlock to extirpation. HWA poses a significant threat to these eastern US natives, now infesting hemlocks across 19 states and more than 400 counties. For the long-term preservation of the species, ex situ genetic resource conservation efforts such as seed collection, storage, and adelgid-resistant hemlock breeding may all be necessary. To ensure the efficient and effective application of these efforts, it will be necessary to prioritize locations within the native ranges, because it is logistically impossible to apply these efforts to all populations. To build upon 12 years of seed banking for eastern and Carolina hemlock, we applied a novel approach for incorporating multiple dissimilar data sets into a geographic prioritization of areas for the most effective and efficient conservation of genetic diversity. The approach involves integration of geographic information systems with the multi-attribute frontier mapping technique to Electronic supplementary material The online version of this article (identify locations across the ranges of these two imperiled species most in need of conservation actions. Specifically, our assessment incorporated four genetic diversity parameters, a climate component, a measure of population disjunctiveness, a measure of local hemlock abundance, and seed collection density to prioritize areas of eastern and Carolina hemlock occurrence for ex situ gene conservation. For each species, the result was a mapped index of locations prioritized by the combined significance of these factors. For eastern hemlock, this assessment assigned the highest priority to disjunct populations and to some areas within the main-body range. With Carolina hemlock, disjunct northern populations and central main-body locations received the highest prioritization. Our prioritization approach could be applied similarly to other species facing pressure from invasive pests or other environmental threats.