Beside natural selection, today's cultivated crops have experienced two types of strong artificial selections: domestication and modern breeding. Domestication has led to a giant genetic structure differentiation between cultivars and their wild relatives, and modern breeding has created further genetic structure differentiation between the modern varieties and the landraces. In a genome, genetic diversity at a locus experienced strong selection is significantly lower than that at other loci non-experienced selection and diversities in the flanking regions also declines. This phenomenon is called the hitchhiking effect or genetic selection sweep. The genomic regions with selection sweep could be detected through scanning a number of released varieties or natural populations with molecular markers. Thereafter, agronomic important traits linked with these regions could be detected using Marker/Trait association analysis. Fine scanning of these genomic regions would help to determine the sizes of these regions and to discover the favorable alleles or even the key genes. This could provide very valuable information for gene isolation and molecular design of new varieties. Establishment of high density genetic linkage maps in the major crops and availability of high throughput genotyping platform make it possible for discovering agronomic important genes through marker/trait association analysis. Based on the available publications, we give a brief introduction of the hitchhiking effect mapping approach using the plant height, 1000-grain weight, and phosphorus-deficiency tolerance as examples in wheat.