Population growth, urbanization and agriculture lead to degradation and loss of natural environment. This has an adverse effect on the diversity of habitats, species and genes and might cause decline in the quality of life of the resident population. In this context and in the densely populated Geneva cross-border area, we study biodiversity dynamics and the effect of the environment on the distribution of genetic variation (URBANGENE project). We use genetic information of three model species (a plant, an insect and an amphibian) in combination with environmental and landscape data to evaluate their potential to disperse and adapt to urban environments. Based on a representative population survey, we further investigate how urban residents perceive their quality of life with a local biodiversity perspective, compared with health data measured in the same areas. Using genome-wide SNP data, we assessed genome-environment associations for Plantago major, a synanthropic plant, in order to obtain information on its ability to disperse among habitats and to adapt to the urban environment. Butterfly (Pieris rapae) and amphibian model species (Bufo bufo) will be sampled in 2015. As regards the amphibians, we developed a WebGIS participatory platform, making it possible for Geneva residents to indicate the geographic location of amphibian habitats on an interactive map, and to transmit information on the species they observed in this area. The integration of results from this interdisciplinary project should allow for a more sustainable urban development and a better conservation and management of biodiversity in urban areas.