1. The current rate of species loss calls for immediate actions to preserve biodiversity and ecosystem functioning. Cataloguing species richness and composition, and revealing how diversity is geographically distributed are the first steps towards designing efficient conservation strategies. 2. Here, we aim to determine diversity patterns and potential drivers of taxonomic and genetic diversity and population structure of Iberian spiders. We used a community level perspective, analysing more than 3000 DNA barcode sequences representing similar to 370 spider species dwelling in white-oak forest habitats across the Spanish National Park network. 3. By combining and comparing morphological and DNA barcode-based species delimitation methods, we assessed their performance and identified putative factors behind cases of incongruence. Our findings uncovered potential overlooked diversity as suggested by the geographic patterns of genetic variation and put a red flag on those taxa that may be undergoing overlooked evolutionary or ecological processes. 4. Spider functional traits associated with foraging strategy, microhabitat preference, ballooning ability and circadian activity explained the observed patterns of population structure across species but did not explain variation in genetic diversity. Overall, our study represents a major step forward in the understanding of large-scale diversity patterns in Iberian spiders at the community level and provides relevant information to guide future conservation strategies of the so-far largely overlooked invertebrate diversity.