High mountain ecosystems are hotspots of biodiversity that are highly vulnerable to climate warming and land use change. In Europe, high mountain habitats are included in the EC Directive 92/43/EEC (Habitats Directive) and the identification of practices facilitating effective monitoring is crucial for meeting HD goals. We analyzed the temporal changes in species composition and diversity on high mountain EU habitats and explored if the subgroup of diagnostic species was able to summarize the comprehensive information on plant community variations. We performed a re-visitation study, using a set of 30 georeferenced historical plots newly collected after 20 years on two EU habitats (Galium magellense community growing on screes (8120 EU) and Trifolium thalii community of snowbeds (6170 EU)) in the Maiella National Park (MNP), which is one of the most threatened Mediterranean mountains in Europe. The presence of several endangered species and the availability of a botanical garden, a seed bank, and a nursery, make the MNP an excellent training ground to explore in situ and ex situ conservation strategies. We compared overall and diagnostic species richness patterns over time by rarefaction curves and described the singular aspects of species diversity (e.g., richness, Shannon index, Simpson index, and Berger–Parker index), by Rènyi’s diversity profiles. Diversity values consistently varied over time and across EU habitat types, with increasing values on scree communities and decreasing values on snowbeds. These changes could be associated with both land use change, through the increase of grazing pressure of Apennine chamois (Rupicapra pyrenaica ornata), which determined a rise of nitrophilous species in the scree community, and an increase of grasses at the expense of forbs in snowbeds, and to climate change, which promoted a general expansion of thermophilous species. Despite the two opposite, ongoing processes on the two plant communities studied, our results evidenced that diagnostic species and overall species followed the same trend of variation, demonstrating the potential of diagnostics for EU habitat monitoring. Our observations suggested that the re-visitation of historical plots and the implementation of frequent monitoring campaigns on diagnostic species can provide important data on species abundance and distribution patterns in these vulnerable ecosystems, supporting optimized in situ and ex situ conservation actions.