There are a large number of advanced genes in crop germplasm resource groups . The rich genetic variations in crop germplasm resources groups have been also failed to fully explore and utilize because of being lack of appropriate statistical methods. Linkage disequilibrium analysis is a effective way to identify the function of the of the gene (or targeted high-resolution QTL). Development of DNA sequencing technology and high-throughput SNP analysis technology make it possible that discoverys excellent genes by using linkage disequilibrium.This article summarizes the research of exploring excellent genes with linkage disequilibrium in crop germplasm resources groups.