Further biogeographical studies of parasites are vital to improve our understanding of biodiversity distribution and predict the impacts of global change. Hypersaline lakes are good laboratories to investigate the avian cestode abundance and species diversity given the abundance of hosts (waterbirds and Artemia) and their broad latitudinal distribution. We analysed cestode infection in brine shrimp Artemia franciscana in northern (Atacama) and central Chile and compared them to results from A. persimilis in southern Chile (Patagonia). Thus, we covered a broad latitudinal gradient from 23° to 53° S. Five cestode taxa including two species of the genus Flamingolepis, Gynandrotaenia stammeri, Eurycestus avoceti, and Fuhrmannolepis averini were recorded from A. franciscana in Atacama lagoons (prevalence = 4.1%). In contrast, no cestode infection was detected in central Chile, likely because they are temporary wetlands. Parasites of flamingos and shorebirds were associated with Atacama lagoons (arid and higher salinity), while Confluaria podicipina and Fimbriarioides sp. (parasites of grebes and ducks, respectively) were dominant in Patagonian lagoons (sub-antarctic and of lower salinity). These differences mirror changes in the relative abundance of the respective final hosts. The flamingo parasite Flamingolepis sp. 1 was the most prevalent and abundant cestode in Atacama, where it was recorded only in autumn. Seasonality and habitat effects (especially abundance and phenology of different bird species) appear to override any latitudinal trends in the prevalence, diversity, and distribution of cestodes. Cestode prevalence was higher in larger wetlands but was not related to the sex of either intermediate host. We recorded a greater taxonomic richness at the cestode family level in Atacama, but a greater dominance of a single family of avian hosts (the flamingos). Ours is the first spatio–temporal study of Artemia cestodes at local and regional scales in the southern hemisphere.