Aquatic ecosystems are characterised by strong trophic links, which can be profoundly altered by the loss or introduction of species. Invasive species that displace key native species may indirectly affect entire communities and ecosystem functioning. Introduced species often show distinctive traits that facilitate their success, such as reduced susceptibility to parasites that commonly infect native hosts. Here, we examine the ecological consequences of the invasion of the American brine shrimp Artemia franciscana on the native clonal species Artemia parthenogenetica and their cestode parasites in a hypersaline ecosystem. We carried out monthly sampling (January-June) in Odiel saltpans to compare Artemia population structure and cestode infections before (2011) and immediately after (2016) the invasion, quantifying host density, biomass and parasitological status. A. franciscana dominated and reached significantly higher densities than the native Artemia by the end of the spring 2016. Although both hosts shared the same parasite species, infection levels were markedly higher in the native species (47.33% vs. 5.30% prevalence). The cestode Flamingolepis liguloides was 18 times more frequent and induced stronger pathological effects (higher rates of castration and red colouration) in native Artemia. Invasive hosts showed a higher proportion of dead F. liguloides cysticercoids. The shift in dominant Artemia species is likely to affect other community members and ecosystem processes, given the keystone role of Artemia in hypersaline ecosystems. Our results highlight the importance of changes in host availability and host-parasite dynamics that can cascade through communities and influence entire ecosystems, particularly in the context of biological invasions.