Having clear ecological knowledge of protected species is essential for being able to successfully take actions towards conservation, but this knowledge is also crucial for managing and preventing conservation conflicts. For example, the Siberian flying squirrel, Pteromys volans, listed in the EU Habitats Directive and inhabiting mature forests that are also the target for logging, has had a major role in political discussions regarding conservation in Finland. This species has also been well-researched during recent decades, providing knowledge on the ecology and management of the animal. Herein, we review knowledge on habitats, demography, community interactions and spatial ecology of this flagship species. We compare the ecology of flying squirrels with that of other arboreal squirrels, and summarize conservation management and policy related to flying squirrels. Reviewed research on the Siberian flying squirrel shows that the species has many similarities in behaviour to other arboreal squirrels. For instance, arboreal squirrels deviate from the general pattern of male-biased sexual size dimorphism in mammals, which perhaps relates to the mating system of arboreal squirrels. Important differences are found in the response of Siberian flying squirrels to tree mast, i.e. pulsed food resource, compared to that of red squirrels, and in communal nesting behaviour compared to that of North American flying squirrels. The extensive knowledge on dispersal behaviour of the flying squirrel, well-studied habitat associations and the proved need for evidence-based conservation may guide researchers and managers working with other similar species. For conservation, the case of the Siberian flying squirrel demonstrates that habitat protection becomes both ineffective and uneconomical if ecological knowledge is not applied in the conservation planning process. The cost-effective conservation of the species requires both landscape-level conservation planning and flexible conservation options to increase the motivation of land owners for conservation.