Aegla alacalufi and A. neuquensis are exclusively found in freshwater systems of Patagonia. The geographic distribution range of A. alacalufi is vast and fragmented, covering continental and insular rivers. A new record of this species on Duque de York Island (50°34′S-75°20′W) defines the southernmost limit for the distribution of freshwater anomuran crustaceans. Aegla neuquensis is only found in Extra-Andean Patagonian rivers. The current geographic distribution patterns of these species can be explained by the existence of multiple island glacial refuges during the Last Glacial Maximum and by the hydrographic captures that occurred during the Late Glacial.