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The genomes of six populations were screened using microsatellites as molecular markers,including Ujmuqin sheep,small-tailed Han sheep,Tan sheep,Hu sheep,Tong sheep and Yangtse River Delta (YRD) white goat.A total of seven microsatellite markers were used and genetic diversity and genetic distance were also determined.The results showed that there were 224 alleles in six populations,all seven loci showed polymorphism in all populations.The average heterozygosity of all populations was 0.949 9,and the mean polymorphism information content (PIC) of all six populations was 0.842 5-0.929 4.The six sheep (goat) populations were lowly differentiated with all loci,and the coefficient of phaenotype differentiation (Fst) was 2.6%,which was consistent with the coefficient of gene differentiation (Gst).The global heterozygote deficit across of all populations (Fit) amounted to 0.5%.The overall significant deficit of heterozygotes because of inbreeding within breeds (Fis) amounted to -2.2%.Two Unweighted Pair-group Method using Arithmetic Averages (UPGMA) dendrograms were constructed on the basis of Nei’s standard genetic distance (DS) and Nei’s genetic distance (DA) respectively.Hu sheep and Tong sheep were grouped at first,Ujmuqin sheep and small-tailed Han sheep clustered and then clustered with Tan sheep.Finally,Yangtse River Delta white goat joined in with all above.From this study,Ujmuqin sheep belongs toMongolia sheepgroup,which corresponds with the historical records exactly.Ujmuqin sheep and small-tailed Han sheep,Tan sheep,Hu sheep and Tong sheep all vest in theMongolia sheepgroup.