The puna is an ecosystem located in the desert plateau above 3500 m elevation in the Andes Range that covers parts of north- eastern Chile, north-western Argentina, south-eastern Peru and mid-western Bolivia between 15° and 28° S latitude. Laguna Lejía is a shallow lake set in an endorheic basin, with high altitude steppe climate type, low temperatures and wide diurnal variation. Precipitation is concentrated in the summer; evaporation is very high and the relative humidity of the environment very low. The object of this study was to characterise the flora and plant associations present in this high, arid ecosystem. Intensive collecting and surveying was carried out in 2008, with the following products: (a) a catalogue of flora, including phytogeographic origin, life form, endemism and conservation state; (b) a phytosociological catalogue, and the characterization of the plant communities with their alpha and beta diversity. Thirty species of vascular plants were recorded, all native. Two plant associations were identified:Pappostipa-Deyeuxia (high Andean scrub) and Puccinellia-Calandrinia, corresponding respectively to the sub-desert steppe of the Atacama puna and the azonal vegetation associated with the Laguna Lejía wetland. The results justify the designation of the area as a priority conservation site for biodiversity by the government.