Abstract: Macrobrachium nipponense is one of the most important freshwater prawns for aquaculture in China,especially in the southern regions of the country.But in recent years,M.nipponense farming has seriously declined due to diseases and small body size.Investigation of genetic background and genetic selection may help this situation for M.nipponense,and development of genetic marker is the basis.Single nucleotide polymorphisms(SNPs) is a type of genetic marker based on single DNA base differences between individuals at defined positions.The possible alleles for a SNP locus are four bases of A,T,C and G.SNPs is a new molecular marker with high value because of its abundance,genetic stability and easy to check.In agricultural economical animals,SNPs were developed in livestock,domestic birds as well as aquatic animals,including fish,shrimp,crab and shellfish.The reported applications of SNPs included determination of relativeness,survey of genetic polymorphisms,QTL localization,marker-assisted selection,etc.So far,no work was reported on development and application of SNPs in M.nipponense.Nuclear rDNA internal transcribed spacer(ITS) were composed of ITS1 fragment between 18S and 5.8S rRNA and ITS2 fragment between 5.8S and 28S rRNA.In this paper,ITS1 sequences were analyzed and SNPs in ITS1 were screened in M.nipponense.Totally 32 samples was sequenced,and the average length of ITS1 sequence was 1749.8bp,which was the longest among reported ITS1 sequences.The average contents of A,G,T and C was 29.9%,28.3%,27.7% and 14.0% respectively,and that of G+C was 42.3%.By comparison of sequences from different individuals,22 SNP loci were found,including 9 C/T transitions(40.91%),4 A/G transitions(18.18%),2 A/T transversions(9.09%),5 T/G transversions(22.73%),1 A/C transversions(4.55%),1 A/T or C transversion(4.55%).Among 22 SNP Loci,21 loci were two alleles,and 1 was three alleles.In addition,3 SSR loci with polymorphisms,1 highly variable segment(243―384 bp),and a great deal of deletions and insertions were found in the ITS1 sequences of M.nipponense.Total 130 deletions and 124 insertions were found,and deletion length was between 1―13 bp,insertions length between 1―80 bp.This paper firstly analyzed the ITS1 sequence of M.nipponense,and filled the gap of its ITS1 characterization,and it also filled the gap of SNP loci development in M.nipponense,and provided new available molecular markers for research of genetics and genetic breeding in M.nipponense.