Haplotype is the combination of a series of genetic mutations that coexist on a single chromosome, each of which has its own unique haplotypes. As a common data analysis method, the analysis of haplotype is effective for the localization of heterozygosis SNPs on single chromosome, the excavation of disease genes and the search of maladies treatments. It mainly includes indirect computational inferential method and direct experimental method. In this review we introduced various haplotype analysis methods and applications, especially two important ones: single-molecule dilution and contiguity-preserving transposition sequencing common technology. Meanwhile, further research prospects on haplotype sequencing were proposed.