To reveal the genetic background of black rice materials and clarify the genetic relationship between the materials, 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) were analyzed by using 30 SCoT primers screened in the laboratory. The results showed that a total of 194 bands were amplified by SCoT primers, including 165 polymorphic bands, and the proportion of polymorphisms was 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 genetic similarity coefficients of the tested rice germplasms were 0.3798 to 0.9697. The results of cluster analysis showed that at a genetic similarity coefficient of 0.73, the 90 rice materials were clustered into four groups. The results of population structure analysis and cluster analysis were in good agreement. This study provides a reference for parental selection in black rice crossbreeding, and a theoretical basis for genetic improvement and cultivation of new varieties of black rice varieties.