Urbanization threatens biodiversity worldwide and is expected to increase in the future. This involves intensification of fragmentation and increase of urban forest remnants. Thus, it is important to understand the functioning of these patches for the preservation of local biodiversity. Mutualistic interactions such as seed dispersal have a key role in the dynamics of plant populations and could help to mitigate the negative effects of fragmentation on wild plant populations. In this context, we have used the mastic Pistacia lentiscus, a common Mediterranean shrub, as a model to study the interaction between seed dispersal by birds and the local genetic diversity of individuals in a highly fragmented semiarid forestry area of the Iberian Southeast (Murcia, Spain). Results reveal a high genetic diversity and a lack of differentiation between shrub patches of P. lentiscus in the area, probably as a result of a strong, but rather recent fragmentation, and an apparently poor contribution of birds to the dispersal of Pistacia seeds. However, the existence of latent impacts cannot be discarded, since at least one of the patches shows some signs of inbreeding.