Colombia has a very rich tree flora, with almost 6,000 species registered to date. The country also has high tree endemism. As a contribution to the “Global Tree Assessment”, we assessed 860 species to complete the red list of the 1,148 endemic trees of Colombia. To categorize the species according to the IUCN red list guidelines, we used geographic occurrences obtained from herbarium-specimens. We carried out detailed analysis of habitat quantity and quality (using forest cover and human footprint maps) and documented anthropogenic threats and conservation actions. Almost half of the endemic trees were categorized as threatened (41% of the assessed, and up to 49% for all species). Most species had small distributions, with an average of 6.2 known populations. Endemic tree occurrences were more common in the Andes and Magdalena regions, which have very high human footprint and consequently a large proportion of threatened species. The major threat to endemic trees was habitat destruction, due mainly to deforestation for livestock and crops. Many endemic trees were present in protected areas (65%), but threatened and non-threatened species had low coverage under protection and many of their populations persist in disturbed habitats. The red list assessments are being used for the difficult task of spatial conservation planning in a megadiverse country, for example by identifying Key Biodiversity Areas and Important Plant Areas. Colombia has hundreds of threatened endemic trees, most of them in global biodiversity hotspots, with very few proactive conservation actions. It is urgent to increase the coverage of endemic tree populations in effectively-managed area-based conservation measures and to complement this with exsitu and other conservation actions. There are conservation action plans for a few timber species in the country, but these efforts need to be supported more widely and extended to other less charismatic groups of trees.