Due to their static nature, protected areas (PAs) are vulnerable to global change, and resident species will likely need to colonize new sites and exchange migrants to sustain viable local populations. Alpine habitats often have a high level of protection, yet extensive environmental heterogeneity and the limited dispersal ability of many endemic species makes it unclear whether PA networks provide sufficient connectivity to protect vulnerable species. We assess landscape connectivity in the European alpine PA network by combining measures of habitat and genetic connectivity using community landscape genetics approaches. Examining 27 plant species, we compare levels of genetic diversity in PA and non-PA sites, and rank non-PA sites for their potential value in facilitating genetic and habitat connectivity, as well as preserving species richness in 893 alpine plants. Non-PA sites do not significantly enhance overall levels of genetic variability across species. However, spatial genetic turnover (allele frequency variation across space) is influenced by geographical and environmental distance, suggesting that genetic connectivity, and by extension landscape connectivity, is impacted by gaps in the PA network. A subset of non-PA sites, when measured for habitat connectivity, genetic connectivity and species richness using spatial graphs, substantially increase landscape connectivity for alpine plants, although there are discrepancies among metrics in ranking sites. We provide the first example of the evaluation and prediction of new PAs including levels of intraspecific genetic diversity for a whole community. This has significance for the management and extension of the European alpine network, especially in identifying valuable unprotected sites.