Habitat loss and fragmentation are interdependent processes, the former referring to decreased area of habitat in the landscape and the latter to separation of habitat to fragments. For conservation they may imply a need for different kind of management actions. When fragmentation poses problems, managers should, for example, ensure that individuals are able to move between habitat fragments. If fragmentation is not a threat, then managers can concentrate on quality and amount of habitat in the landscape. We review research related to these factors for the Eurasian red squirrel, Sciurus vulgaris and the Siberian flying squirrel, Pteromys volans. The reviewed studies indicate that these species are not very sensitive to habitat fragmentation, mainly because individual’s ability to move and disperse in fragmented landscapes is relatively good. For both species, many landscapes are functionally continuous, i.e. individuals can reach most habitat fragments in the landscape. However, in agriculture-dominated areas, large open areas may restrict their movements and, indeed, heavy fragmentation by agriculture has been shown to affect red squirrel populations. We conclude that when planning conservation practices for both squirrel species, the best option would be the management aiming to increase the amount and quality of suitable habitat. However, currently it is not possible to predict when the effects of fragmentation start to aggravate the effects of habitat loss for squirrel populations.