Most agronomic traits such as yield, quality and stress-tolerance of crops are quantitative traits. It is not easy to dissect genetic basis of these traits because they are controlled by multi-genes that are affected by environmental factors. Hitchhiking mapping offers a new method for identifying of loci controlling those traits and assessing their allelic variations. Marker-trait association analysis based on the hitchhiking effects will play an important role in dissection of complex traits. Combination of quantitative trait loci (QTL) mapping with marker-trait association analysis will facilitate dissection of complex traits, resulting in important information and markers for molecular breeding by design in crops. In this review, we presented a brief introduction of hitchhiking effects, marker-trait association analysis and practical considerations.