The Carpathians are the largest mountain range in Central Europe. Their geographical position, extent, isolation, landscape heterogeneity, well‐preserved environment, and relatively low impact of Quaternary glaciations make them of utmost importance for studies on European biodiversity and biogeography. In this review, introducing a Special Issue of the Biological Journal of the Linnean Society, we provide an overview of current research and focus on three main aspects: (1) distribution patterns and species richness including endemism; (2) phylogeographical patterns, inference of major barriers, and divergence areas; and (3) cytological studies and cytogeography inferred from vascular plant polyploid complexes. Our survey shows that, although accurate estimation is not possible for several important taxonomic entities because of unavailable or dispersed data, the Carpathians are a clear hotspot of European diversity for many groups of organisms, such as mammals, breeding birds, amphibians, lichens, and vascular plants. Certain groups, not necessarily those with high species richness, are rich in endemic taxa. This holds mainly for subterranean invertebrates, molluscs, grasshoppers, beetles, spiders, and vascular plants. Distribution patterns of endemic richness vary across taxonomic groups, as well as geographically, reflecting both history and habitat features. In general, the South‐Eastern Carpathians have a significantly higher proportion of endemic taxa than the northerly‐situated Western Carpathians. Molecular clock‐based estimations have provided some insight into the diversification age of the Carpathian biota, including a Tertiary origin for some endemic taxa and lineages, especially those confined to environmentally stable habitats. Distribution patterns, as well as phylogeographical and phylogenetic data, corroborate the persistence of many high‐mountain and forest taxa during the Quaternary climatic oscillations, often in multiple spatially delimited areas isolated by physical barriers. Several studies show that the Carpathian massifs played an important role as refugia for rare lineages and/or as stepping stones in migrations. Phylogeographical analysis reveals clear patterns of biogeographical breaks, as well as links, although clear exceptions also confirm that extant distribution patterns are often shaped more by idiosyncratic processes acting at different geological times. Cytogeographical data also uncover several consistent patterns, which probably reflect a deeper evolutionary history. In conclusion, the available data highlight the unique position of the Carpathians in the evolution and preservation of European biota within the European Alpine System.