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Abstract: Haplotype block partition has become a very interesting topic recently due to its potential applications in haplotype-SNP based association study. In this talk, I will present a new block parition method based on pairwise linkage disequilibrium (LD). Both simulated and real data have shown that the new algorithm has a higher power than some existing methods in estimating blocks. To measure the similarity between dierent partitions fairly, a new statistic will be introduced. It can also be used to measure the accuracy and self-consistency when using dierent sets of SNPs by the same partition method. I also want to draw the attention to the maker density issue. By onl