Abstract: For the purpose of new varieties(lines) identification at the molecular level, 11 pairs of SSR(Simple Sequence Repeats) primer markers were employed to analysis of genetic and construction of fingerprinting for 9 new potato varieties and its parents in Fujian.. The results showed that, 89 alleles loci were amplified, including 84 polymorphic alleles, and the ratio of polymorphism reached 94.38%. The numbers of alleles site amplified with different primers was 5-15, and the average value was 8.09. The fingerprinting of 13 potato varieties was constructed by 6 pairs of primers,STI027, STI052, STI033, STI047, STM3023, and STM0030. All the potato varieties were univocally identified using SSR primer STI027, and ten potato varieties were univocally identified using SSR primer STM0030. UPGMA cluster analysis of genetic similarity showed that all the materials were clustered into four groups at the genetic similarity of 0.628. The cluster analysis result was accordance with the genetic relationships.