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Urban reserves, like other protected areas, aim to preserve species richness but conservation efforts in these protected areas are complicated by high proportions of alien species. We examined which environmental factors determine alien species presence in 48 city reserves of Prague, Czech Republic. We distinguished between archaeophytes, i.e. alien species introduced since the beginning of Neolithic agriculture up to 1500 A. D., and neophytes, i.e. modern invaders introduced after that date, with the former group separately analysed for endangered archaeophytes (listed as C1 and C2 categories on national red list). Archaeophytes responded positively to the presence of arable land that was in place at the time of the reserve establishment, and to a low altitudinal range. In addition to soil properties, neophytes responded to recent human activities with the current proportion of built-up area in reserves serving as a proxy. Endangered archaeophytes, with the same affinity for past arable land as other archaeophytes, were also supported by the presence of current shrubland in the reserve. This suggests that for endangered archaeophytes it may have been difficult to adapt to changing agricultural practices, and shrublands might act as a refugium for them. Forty-six of the 155 neophytes recorded in the reserves are classified as invasive. The reserves thus harbour 67% of the 69 invasive neophytes recorded in the country, and particularly worrisome is that many of the most invasive species are shrubs and trees, a life form that is known to account for widespread invasions with high impacts. Our results thus strongly suggest that in Prague nature reserves there is a high potential for future invasions.