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Antarctic and Subantarctic lakes are unique ecosystems with relatively simple food webs, which are likely to be strongly affected by climate warming. While Antarctic freshwater invertebrates are adapted to extreme environmental conditions, little is known about the factors determining their current distribution and to what extent this is explained by biogeography or climate. We explored the distribution of freshwater crustaceans (one of the most abundant and diverse group of organisms in Antarctic and Subantarctic lakes) across four biogeographic provinces (Continental Antarctic, CA; Maritime Antarctic, MA; Subantarctic islands, SA; and Southern Cool Temperate, SCT) based on the literature, predicting that species distribution would be determined by biogeography, spatial autocorrelation among regions (in relation to dispersal) and climate. We found that variation in species composition was largely explained by the joint effect of spatial autocorrelation and climate, with little effect of biogeography - only regions within the SA province had a clearly distinct species composition. This highlights a plausible main influence of crustacean dispersal - mainly through migratory seabirds - and suggests that some regions will be more affected by climate warming than others, possibly in relation to the existence of nearby sources of colonists.