The superior and/or novel alleles (even rare alleles) for a particular trait are often detectable in crop germplasm resources. Exploration and application of allelic variations in crop genetic improvement is one of the tasks in the field of germplasm resources. Allele mining, which is an important tool in deciphering the genetic diversity, the origin and evolution, the molecular mechanism of important agriculture traits as well as germplasm innovation, etc., is the cornerstone of crop breeding by molecular design. There is a great demand on development of high-throughput, efficient allelic mining approaches, in order to accelerate the discovery of excellent alleles and their application in future crop improvement. For this purpose, here we review the major methods of the allelic discovery and propose the research priorities and focuses.