Identifying and protecting key areas for biodiversity is a cornerstone of effective nature conservation. This conservation assessment analyzes 77 ecoregions across the southern, settled part of Canada to identify priorities for conservation action. Our analysis included 34 measures of biodiversity, threat and conservation response. We categorized all ecoregions based on their overall biodiversity and threat scores. This categorization identified nine “crisis ecoregions.” These ecoregions have higher biodiversity and threat scores compared to other ecoregions in the study area. These ecoregions represent less than 5% of Canadian lands and inland waters but provide habitat for over 60% of Canada’s species at risk. Twenty-one ecoregions have higher biodiversity but lower threat scores. Primarily distributed in the more intact portions of the study area, these ecoregions generally have lower biodiversity scores for species diversity, but score very high for intactness, habitat diversity and congregatory species. This assessment can help to contextualize existing and proposed conservation actions by highlighting key biodiversity, threat and conservation attributes of ecoregions across southern Canada. Our assessment can be used to focus efforts on new protected areas, species at risk recovery, capacity building and ecological monitoring. The results of the conservation assessment can be applied to set and track progress toward national, regional and organizational conservation goals, including post-2020 biodiversity targets. Regular reanalysis of the ecoregions to track their trends in biodiversity, threat and conservation responses will support monitoring the effectiveness of conservation programs and highlight ecoregions where continued focus is most needed to conserve Canada’s biodiversity.

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Over 90% of recent human-caused extinctions are wild species known from only one nation. These nationally endemic species represent one of the greatest global conservation responsibilities for any country. To meet this responsibility, we must first identify nationally endemic species. We developed the first comprehensive inventory of the 308 plant, animal, and fungi species and infraspecies only found in Canada, of which approximately 90% are of global conservation concern. Our analysis also identified 27 spatial concentrations of endemic species, many of which are associated with glacial refugia, islands, coasts, and unique habitats. Nationally endemic species have not been the primary focus of endangered species conservation in Canada and other countries.Our analysis provides a case study on how national inventories of endemic species can be developed and applied to support species assessments and place-based conservation. Prioritizing endemic species for conservation can build on sentiments of sense of place and national responsibility to foster public interest. We propose a species conservation framework that highlights the critical role of national endemism in preventing global extinctions. Greater conservation focus on endemic species will support national and international biodiversity conservation targets, including the post-2020 Global Biodiversity Framework.