Considering the complexity of black rice germplasm resources on distribution and origin， uncovering the genetic diversity of black rice materials and clarify their genetic relationship becomes of significance. This study analyzed the genetic diversity of 90 rice materials （including 21 black leaf black rice， 24 purple leaf black rice， 30 green leaf black rice， and 15 white rice） by using 30 SCoT primers. A total of 194 fragments were detected by SCoT primers， including 165 that showed polymorphic with the ratio of 85%. The average values of allele number （Na）， effective allele number （Ne）， Nei′s gene diversity index （H） and Shannon′s information index （I） were 1.9216， 1.3922， 0.2445 and 0.3836， respectively. The results of cluster analysis showed that at a genetic similarity coefficient of 0.73， these genotypes were clustered into four groups， coincidence with the results of population structure analysis. The genetic similarity coefficient predominantly ranged from 0.59 to 0.79， indicating a relatively high genetic similarity. Analysis of molecular variance（ANOVA） showed that 91% of the genetic variations were within the population， with only 9% being between the populations. These findings indicate that there is limited genetic diversity in the collection， and enriching genetic diversity of black rice germplasm resources required further efforts. This study provides valuable insights for parental selection in black rice hybridization， and offers a theoretical basis for genetic improvement and cultivation of new black rice varieties.