AbstractGenetic diversity represents the fundamental basis of biological variation within species, and is therefore the ultimate representation of biodiversity. Despite that all forms of diversity being defined by genomic differences, genetic diversity has received relatively less attention compared with species and ecosystem diversity. Here, we review recent literature and conclude that progress in understanding genetic diversity of seed plants is strongly associated with advances in sequencing technology. We here present case studies to illustrate the application of genetic diversity for tracing crop domestication and delimiting species boundaries. Understanding genetic diversity is particularly critical for the field of conservation biology, and there is a clear shift to population‐level genetic studies to understand rare species. We then document additional factors that potentially influence genetic diversity, including climate change, habitat fragmentation, and species invasion. Finally, we identify current research limitations and propose directions for future studies. We highlight the need to develop broad‐scale genetic diversity knowledge, combined with other aspects of diversity to improve biodiversity conservation outcomes. We conclude that populating global databases with genomic‐scale sequence data for all species is an urgent and achievable goal now.