Wolves have been coming back for several years in the southern French Alps. In two valleys of the Mercantour national park, they have been present for 15 years. Sheep farmers have to adapt their farming systems to this presence. We carried out surveys among the sheep farmers i) to describe the strategies they adopt to protect flocks ii) to pinpoint the organisational effects that these strategies have on the pastoral system. We studied immediate and mid term effects of this presence on sheep farming systems. Sheep farms are maintained on this area but this is due to a lack of alternatives for sheep farmers. Over the medium term, this questions the maintenance of sheep farming. Our surveys also underline specific difficulties for some farming styles in adapting to these new production contexts. So over the medium term the diversity of farming systems will be re-defined. In the short term, the adoption of the protection plan is a major disruption of the pastoral system. Gathering flocks into a night paddock in particular is not considered by the farmers as relevant to their local know-how. The result emphasises the difficulties in reconciling the organisational flexibility needed by the pastoral sheep system with the rigidity of the norms defined for the protection plan as administratively defined. The obligation for breeders to conform to such a plan has as a consequence a loss of farmer control concerning interactions between flock and grazed territory. Our results underline the need to reconcile these contradictions to ensure a positive contribution of sheep farming to biodiversity conservation policies in pastoral landscapes.