Knowledge of the conservation status of the native flora at an administrative level, such as the regional level, is useful to take actions to reduce biodiversity loss at a local level. In this study, we classified the native flora of the Arica-Parinacota and Tarapaca Regions according to its conservation status using a database of 7,432 geo-referenced records corresponding to 717 native vascular species. The classification was carried out using mainly geographical criteria of IUCN (version 3.1). A 27.6% of the native species in these regions have conservation problems (3.2% Endangered and 24.4% Vulnerable). In the Arica-Parinacota and Tarapaca Regions, 34.4% and 24.3% of the species, respectively are threatened. The native flora of these two regions has a greater degree of threat than that found in either Antofagasta, Atacama or Coquimbo. This is partially explained by restricted distributions (extent of occurrence and/or area of occupancy) combined with a decline in habitat quality.