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The Puna is a high altitude ecosystem of the Central Andes located in the desert plateaus above 3500 m a.s.l. that covers parts of north-eastern Chile, north-western Argentina, south-eastern Peru and mid-western Bolivia. It is characterised by the presence of endorheic basins. Laguna Lejia is an oligohaline shallow lake with alkaline pH, located in the Atacama Puna above 4000 m a.s.l. It is surrounded by volcanoes and enclosed in a secluded basin that is of great scientific interest, due to its ecological insularity. It has been designated by the government as a priority site for biodiversity conservation. The object of this study was to analyse the specific composition and the structure of the zooplankton community in this shallow, high altitude lake. In March 2012, zooplankton samples were taken for qualitative and quantitative analysis from 13 sampling stations in the lake and two adjacent pools. The bodies of water were characterised in the field using portable equipment, with the following parameters being measured: pH, water temperature, conductivity, and dissolved oxygen. The results indicate that the type of zooplankton community matches relatively well that observed in other low salinity, high Andean wetlands, although no calanoid copepods were found. The species found have been reported for high Andean zones and shallow lakes in countries bordering Chile. The absence of species with wide geographical distribution specific for low salinity, high Andean environments, is presumably due to the presence of geographical and environmental barriers that prevent colonization by those species.