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This paper compares the responses of two contrasting Arctic ecosystems to climate change simulations: a polar semi-desert (in Svalbard) and a dwarf shrub heath (at Abisko, northern Sweden). These ecosystems are located close to the northern- and southernmost extremes of the Arctic region, respectively. Impacts of simulated climatic changes were determined through factorial perturbation experiments, where growing season temperature, nutrient availability and water supply were manipulated. The results are compared with the impact of interannual variation in climate on the growth of a keystone moss species, Hylocomium splendens, from the wider circumpolar area. The perturbation studies revealed that current interannual variability in temperature and the temperate tolerance of many species may exceed predicted changes in mean summer temperature over the next century. Arctic ecosystems differed in their responses to environmental manipulations, with the structure of the dwarf shrub heath being affected through shifts in competitive hierarchy, potentially leading to lower biodiversity, and the polar semi-desert being affected through invasion, potentially leading to higher diversity. H. splendens showed negative responses to perturbation at the sub-Arctic site, in contrast to the positive relationship between temperature and growth observed in the natural environment. This apparent discrepancy may result from: (i) artefacts arising from the perturbations, such as lower atmospheric relative humidity; (ii) non-equilibrium responses during the relatively short-term perturbation studies and/or (iii) ecotypic variation in the moss population. Thus, caution should be employed when extrapolating from perturbations studies to both longer time-scales and different ecosystems within the Arctic.