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Although a large number of rivers stretches in Southeast Europe (SEE) have a pristine status compared to the rest of Europe, these ecosystems and their freshwater biodiversity are perceptibly threatened. Since crayfish species are known to cover a wide spectrum of ecological functions they are considered as keystone species and ecosystem engineers. Therefore, their decline may substantially impair local biodiversity and ecosystem services. In this manuscript we present a brief overview of the status of the native freshwater crayfish and their habitats in SEE. Different forms of physical habitat degradation as well as invasive alien crayfish species and their pathogens (e.g., Aphanomyces astaci) are simultaneously threatening endangered populations all over SEE. Even though all native crayfish species are listed in the IUCN Red List, so far none of the 33 LIFE rehabilitation projects performed in SEE, has crayfish as target species in their agenda. Furthermore, SEE countries rarely designated Natura 2000 sites for native crayfish. We propose future studies to assess the distribution and functional role of crayfish species in SEE, as well as to develop habitat suitability models for these species during future conservation projects.