The Atacama is the world's driest desert. It contains various types of wetlands. In general, the diversity and structure of the zooplankton in these wetlands have been very little studied. The object of the present study was to analyse the specific composition and structure of the zooplankton in a transect which included highland bogs and an endorheic mountain river in the Altiplano of northern Chile. In 2017, samples of zooplankton were collected for qualitative and quantitative analysis in two types of wetlands. Eight taxa of zooplanktonic crustaceans were recorded. The results of null models revealed the absence of regulator patterns for all sites in species co-occurrence. Cluster analysis generated two groups with low similarity between them. The results observed in the correlation matrix showed significant direct associations between some species and the level of dissolved oxygen, conductivity and salinity.