The individual haplotyping MSR(minimum SNP removal)problem is the computational problem of inducing an individual's haplotypes from one's DNA fragments sequencing data by dropping minimum SNPs (single-nucleotide polymorphisms).To solve the problem,Bafna,et al.had provided an algorithm of time complexity O(2^kn²m)with the number of fragments m,the SNP sites n,the maximum number of holes k in a fragment.In the case that there are some Mate-Pairs,since the number of holes in a Mate-Pair can reach 100, Bafna's algorithm is impracticable.Based on the characters of DNA fragments,this paper presents a new algorithm of time complexity O((n-1)(k₁-1)k₂2^2h+(k₁+1)^2h+nk₂+mk₁)with the maximum number of SNP sites that a fragment covers k₁(no more than n),the maximum number of the fragments covering a SNP site k₂(usually no more than 19) and the maximum number of fragments covering a SNP site whose value is unknown at the SNP site h(no more than k₂).Since the time complexity is not directly related with k,the algorithm can deal with the MSR problem with Mate-Pairs efficiently,and is more scalable and applicable in practice.