Urbanization leads to fragmentation, degradation or loss of natural environments and reduces connectivity between remaining habitat patches. This affects dispersal and establishment of species and their genes and might have adverse effects on biodiversity in urban areas. Here we assess functional connectivity between green spaces for one plant (Plantago major) and one insect (Pieris rapae) model species in the Geneva urban area. We also estimate the impact of future urbanization projects planned until 2030 in Geneva (constructions and road projects) on the connectivity network. We show that the connectivity between small green spaces in the urban centres and larger ones in peripheral areas is fragile and unstable. Potential barriers to dispersal for the study species are mainly buildings, roads, but also large areas of forests, crops and vineyards. Furthermore and based on spatially explicit simulations of gene flow, we test how the distribution of genetic variation among populations along rural-urban gradients is affected by urban landscape elements. We compare these results to empirically observed population responses of the butterfly species P. rapae in the region of Marseille, France. For different dispersal scenarios and taking into account the effect of future intensification of urbanization, results show a decrease in genetic diversity in areas characterized by medium to high urban densities. In order to conserve and promote genetically stable and diverse populations, it is therefore important to maintain or increase landscape connectivity, especially between green spaces in dense urban centres and those in more natural peripheral areas.