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Climate change is rapidly affecting the structure and functioning of the tundra ecosystem. The lemming cycles, a key process in this ecosystem, are fading out in many areas of the Arctic. At the same time generalist predators are moving northwards and acting as competitors for genuinely arctic species. Arctic foxes (Vulpes lagopus L.), one of ten climate change flagship species chosen by IUCN, are at the top of the terrestrial tundra food web and sensitive to these changes. The trophic position (i.e. diet) of Arctic foxes, being an opportunistic predator, reflects available prey species and can thus be used as an indicator for monitoring the status of tundra ecosystems. Such monitoring though requires robust methods for diet analysis. Our main objective was to evaluate two different methods of Arctic fox diet analysis based on faces and stable isotopes. We used samples from three sites in low-arctic tundra (Varanger in Norway; Yamal and Nenetskij in Russia). Faeces from each active den in 2007 were analyzed separately and the proportion of dry weight for the different prey categories was calculated. The winter fur, reflecting the diets in previous summer/fall, along with prey samples were collected during summer 2008 and subjected to stable isotope analysis (SIA). The contribution of different food sources to fox diet was quantitatively estimated using a Bayesian mixing model implemented in the SIAR package in the R statistical platform. We also used different prior information (equal “priors” or our knowledge about an ecosystem) and assessed its influence on the resulting diet proportions. Rodent remains vastly dominated in scats for all three sites, but the proportion of lemmings and voles varied: on Yamal Arctic foxes equally used lemmings and voles while in Nenetskij voles strongly dominated over lemmings and the opposite situation was found in Varanger. The configuration of prey in the isotopic space, which is specific for the ecosystem, did not allow estimating their contribution on Yamal with mixture proportions depending strongly on priors. In Nenetskij the configuration of prey in the isotopic space was better than on Yamal and the diet could be assessed with higher precision. SIA showed that voles were the main food source in the arctic fox diet (like it was shown in faeces analysis). In Varanger SIA indicated that reindeer and ptarmigan were important in diet of Arctic foxes and these resources may have been underestimated by the faeces analysis. We show that SIA depends on the configuration of prey isotope signatures and in some cases it is impossible to distinguish between prey groups. This configuration is site specific and may limit the usefulness of SIA in certain cases. The main advantage of SIA is that it reflects assimilated prey resources and can show the importance of prey groups not leaving many remains in the faeces. By combining these two methods we can get a broader picture of the diet variability. This study is a part of the Norwegian International Polar Year project “Arctic Predators”, which was supported by the Research Council of Norway.