Wheat is one of the most important staple crops in the world. However, a series of genetic bottlenecks, such as polyploidization, inbreeding, domestication, and recent improvement, has significantly limited its breeding plasticity, which is crucial to adapt wheat cultivars to rapid population growth and climate change. To recover the lost genetic diversity and lay a foundation for the long-term breeding potential of wheat, we developed the first generation of wheat genetic variation map (VMapI) to evaluate the genetic diversity in wheat and its wild relatives. A total of 420 accessions, representing 24 species and/or subspecies from Genus Triticum and Aegilops, were sampled for whole genome shotgun sequencing. By aligning 20TB reads to the IWGSC1.0 reference genome, about 104 million SNPs were identified from A, B, D sub-genomes. Preliminary analysis showed that the wild relatives of wheat, such as emmer, einkorn, and Ae. tauschii, are generally 2 or 3 time more diverse than common wheat (π = 0.0023). A paralleled selection was also observed in independent domestication processes. While further analysis is being performed, it is anticipated that our study will provide new perspectives on wheat diversity and evolution, and thus be very useful for wheat genetic research and breeding.