European wildcat (Felis silvestris silvestris) populations are fragmented throughout most of the whole range of the sub-species, and may be threatened by hybridization with the domestic cat F.s. catus. The underlying ecological processes promoting hybridization, remain largely unknown. In France, wildcats are mainly present in the North-East and signs of their presence in the Pyrenees have been recently provided. However, no studies have been carried out in the French Pyrenees to assess their exposure to hybridization. We compared two local populations of wildcats, one living in a continuous forest habitat in the French Pyrenees, the other living in a highly fragmented forest-agricultural landscape in Northeastern France to get insights into the variability of hybridization rates. Strong evidence of hybridization was detected in Northeastern France and not in the Pyrenees. Close kin in the Pyrenees were not found in the same geographic location contrary to what was previously reported for females in the Northeastern wildcat population. The two wildcat populations were significantly differentiated (Fst = 0.072) to an extent close to what has been reported (Fst = 0.103) between the Iberian population, from which the Pyrenean population may originate, and the German population, which is connected to the Northeastern population. The genetic diversity of the Pyrenean wildcats was lower than that of Northeastern wildcat populations in France and in other parts of Europe. The lower hybridization in the Pyrenees may result from the continuity of natural forest habitats. Further investigations should focus on linking landscape features to hybridization rates working on local populations.