To evaluate the genetic diversity of major rice varieties registered in Heilongjiang province in the past two decades, 73 conventional rice varieties were collected and genotyped with a set of 62 SSR markers well distributed on all the 12 rice chromosomes, including 24 SSR markers used in rice DNA fingerprint database of China. The results showed that a total of 142 alleles among these varieties were identified at all of 62 SSR markers loci, with an average of 2.3 alleles per marker locus, and 71.0% of the SSR markers were polymorphic between varieties, and the values of the frequency of polymorphism ranged from 0.000 to 0.775 with an average of 0.246. The 73 varieties existed highly similarity, the genetic similarity coefficient ranged from 0.622 to 0.966 with an average of 0.759, and 96.4% of the tested varieties showed the genetic similarity coefficient from 0.66 to 0.86. The 73 varieties were clustered into 11 groups based on the genotyping data, which consisted with pedigree information of these varieties. The major differences among these groups were detected on maturity and grain quality. Based on our results, the genetic background was very narrow in the registered varieties in Heilongjiang province in the past two decades. It is necessary to introgress diversified germplasm and enhance germplasm innovation in the conventional rice breeding program for further increase of rice yield and stress tolerance in Heilongjiang province.