"Threatened species occurrences, Denmark 1991-2015" is the occurrence dataset developed and used during a three-year industrial PhD-project 2015-2018 "Analysis and prioritization of future efforts for biodiversity – with particular regard to Danish Nature Agency lands" (Buchwald 2018). It was used as part of the basis for the 2018 designation of more than 13 000 ha of new forest reserves in Denmark as part of the Danish governments actions to halt the decline in biodiversity in line with Aichi and EU targets for 2020. The PhD-project was conducted in cooperation with the Natural History Museum of Denmark, Center for Macroecology, Evolution and Climate (CMEC) at University of Copenhagen. Study species (N = 1378) were delimited as being terrestrial or amphibious species known from Denmark, and being globally or nationally red-listed in the high threat categories (RE, CR, EN, VU), plus birds listed on Annex I of the EU Birds Directive and species listed on annexes II, IV or V of the EU Habitats Directive. Taxonomy and naming was updated to match the standard species checklist of Denmark maintained by the Danish Biodiversity Information Facility (DANBIF). The quality-checks yielded detailed occurrence data (N= 267,556) for 1,378 species in 24,317 localities counted as different 100 x 100 meter grid cells. One data provider (Fugleognatur.dk) would not let details of the occurences be public, so those observations have details withheld but full details were used in the study.