Gene discovery and allele mining are important in molecular evaluation of crop germplasm resources and are of great practical significance in crop breeding,especially in molecular breeding.Linkage disequilibrium(LD)-based association analysis is an effective approach to find new genes and favorable alleles.In this paper comprehensively basic theories,strategies,characteristics and current successful applications of association analysis in crops were reviewed.The trends and prospects of association analysis were also proposed.It is concluded that with the integration of traditional QTL mapping and functional genomics,association analysis will certainly accelerate the molecular evaluation of crop germplasm resources.