Abstract: The present study aimed to show the application of Mutation Surveyor in analyzing nucleotide substitutions and InDel with an instance. The polymorphisms in ISG15 5′ flanking sequences were analyzed for 144 Hu sheep from Yuhang Hu sheep farm and slaughterhouse by polymerase chain reaction\|single strand conformation polymorphism （PCR\|SSCP） technique， DNA sequencing and Mutation Surveyor software. PCR\|SSCP analysis showed ISG15 5′ flanking sequences bands were too complex to determine genotype directly. The analysis result of Mutation Surveyor found there were three polymorphisms， 152 C/T， 158 dupC and 239 C/T， in ISG15 5 ′flanking region. The frequency of allele C in loci 152 was 083 showing low polymorphism （PIC = 0.2424）. The frequency of allele dupC in loci 158 was 05125 showing mediate polymorphism （PIC = 0.3748）. The frequency of allele C in loci 239 was 07675 showing mediate polymorphism （PIC = 0.2932）. Except 239 C/T， the gene frequencies and genotype frequencies of Hu sheep 152 C/T and 158 dupC tested have reached the Hardy\|Weinberg equilibrium （P>0.05）. Mutation Surveyor software has greater advantage in analysis of nucleotide substitutions， especially InDel sequencing data. So Mutation Surveyor software can be used for SNPs high\|throughput screening and analysis．

Key words: Mutation Surveyor, InDel, ISG15, Hu sheep