Objective of the study was to understand the genetic diversity of millet germplasm resources in Heilongji-ang Province and Jilin Province. Alleles, loci heterozygosity, Shannon's index and effective number of genes（Ne） of20 typical foxtail millets from Heilongjiang and Jilin provinces were analyzed by 5 pairs of SSR primers. Resultsshowed that the number of alleles per primer was 4~6, 26 alleles were obtained, and the average was 5.2. The poly-morphism information content（PIC） of each primer was ranging from 0.645 to 0.767, with the maximum primerEG75638 and the lowest primer QG7172. Loci heterozygosity, Shannon’s index（I） and effective number of genes（Ne） were different in different primers. The highest loci heterozygosity and polymorphism information content ofeach province were derived from different primers, which were JG13656 and DG2831. Cluster analysis of 20 variet-ies of foxtail millet in the genetic similarity coefficient 0.64 showed these varieties could be grouped into 3 catego-ries. The primer analysis of two provinces showed that the genetic diversity of Jilin Province was higher than that ofHeilongjiang Province. Parts of varieties from same geographical got together, it means that genetic relationship wasrelated to geographic origin.