AbstractBranchinecta gaini Daday, 1910 is the southernmost extant Anostracan species occurring in various localities across Maritime Antarctica. Since this region was almost completely glaciated during the Last Glacial Maximum, the identification of potential glacial refugia and the colonization sequence of freshwater habitats within Maritime Antarctica remains primary biogeographic objective for understanding the evolution of the Antarctic environment. To evaluate the history of B. gaini in Maritime Antarctica, we performed phylogeographic analyses of B. gaini and its closest Patagonian congener Branchinecta granulosa Daday, 1902. We sampled 47 populations from all three Antarctic bioregions where B. gaini occurs – South Orkney Islands, North-west and North-east Antarctic Peninsula. B. granulosa was represented by 8 populations from Patagonia. Molecular analyses of two mitochondrial (16S, COI) and one nuclear (ITS2) marker showed low overall mitochondrial variability and the ambiguous nature of ITS2 variability. The species assessment revealed insufficient genetic differentiation between B. gaini and B. granulosa to consider them two separate species. Therefore, the widely accepted idea that there is a species of Branchinecta endemic to Antarctica and sub-Antarctic islands should be omitted, and B. gaini should be synonymized with B. granulosa. Molecular clock analysis of COI for two substitution rates dated the separation of B. gaini from B. granulosa to the Pleistocene (170 – 502 ka BP and 17 – 50 ka BP, respectively). Therefore, Antarctic populations of B. gaini separated from Patagonian B. granulosa before or during the Last Glacial Maximum, indicating an older association with the southern continent than previously anticipated. The geographic distribution of haplotypes further suggests that B. gaini most likely survived at least the last glacial period in an as-yet unknown refugium in Antarctica.