Abstract: The microsatellite (SSR) is a kind of co-dominant, and specialmolecularmarker, and used widely in many ge-netics analysis, such as genetic distance between different populations of organisms. Though papers about the isolation of microsatellite can be often found in journals, no detailed reports about which motif type of microsatellite might be more polymorphism were found so far. Here, we wanted to isolate the microsatllite sequences from random genomic library of Chinese shrimp (F. Chinensis), and obtained polymorphism microsatellite loci, then seek after the correlation between the polymorphism and the repeat motifs of microsatellites. Using the ultrasonic to break the genome DNA, the length of about 800-1500 bp DNA were selected to establish the random clone DNA library, and 1996 sequenceswere sequenced using MegaBace 1000 sequencer (Amersham Biosciences). After the biosoft SeqmanⅡ(DNAstar) assembling, 1990 in-dependent sequenceswere got, and the length of each clone sequence was about 400-700bp, from which 136 microsatel-lite-containing sequenceswere found. W ith the help of primer designed software (Premier Primer 5. 0), thirty-four primer pairswere designed and used to amplify the genome of F. Chinensis by PCR. The criterion for primer design was that the repeat numberofmotifwasmore than fifteen and the length of primer sequenceswas between 20 and 24. The PCR amplifi-cation results were further detected by AgNO3 staining methods and subsequently scanning by scanner. In these primer pairs, the detected results were as following: four primer pairs had no any amplification production, and thirty primers worked effectively, inwhich the polymorphism (allele) was observed. So, the success rate of primer design is88.-%. In the 34 primerpairs, though 30 microsatellite primerpairs generated amplification products, 1-primerpairs got vivid prod-uct bands and abundant polymorphism. So, the method trying to get microsatellite primers from randomly sequenced ge-nome sequences is inefficient. In the research, the lowest repeat numberofmotif is sixteen, and the corresponding number of allele is four. Using SPSS (Version 13. 0), we analyzed further the relationships between polymorphism and types of microsatellite motif, and the resultswere as follows: the polymorphism wasmore for dinucleotide motif than for trinucleoti-de, tetranucleotide, and compound repeat motifs. For the dinucleotide type, there was no significance difference among different classes (i.e. AT, AG, etc.) of dinucleotide motif. Furthermore, we analyzed the correlativity between polymor-phism and the repeat number of dinucleotide motif, and the results showed that there existed correlation between them (r=0.121), but no significance (P=0.621). So, more studies are needed for further clarifying their relationship be-tween polymorphism and types of SSR motif.