<p>Sugar beet is a kind of sugar crop, and sugar, as one of the strategic reserve materials, is of great significance to national development. China is not the origin of sugar beet, sugar beet monogerm germplasm resources are even less. In this study, we evaluated the genetic diversity of 89 genotypes of sugar beet monogerm maintainer line plants using 21 pairs of SSR primers and 34 pairs of InDel primers; a total of 251 pairs of alleles were obtained, with an average of 5.095 alleles per SSR locus and 4.1176 alleles per InDel locus. Based on 21 pairs of SSR markers determination, the gene flow (Nm) among individuals ranged from 0.0711 to 0.5419, with a mean value of 0.1858; based on 34 pairs of InDel markers determination, the gene flow (Nm) among individuals ranged from 0.0059 to 0.6953, with a mean value of 0.1406. Population structure analysis, cluster analysis, and principal coordinate analysis (PCoA) showed that the 89 sugar beet monogerm germplasm could be classified as two taxa PopI and PopII, which in turn could be divided into two subgroups (A and B). The genetic distances of the 89 sugar beet germplasm ranged from 0.1023 to 0.3930, with the genetic distance between germplasm No. 65 in subgroup A and No. 77 in subgroup B the furthest. Distance was the furthest, and these two germplasm were most suitable for breeding as parents. Analysis of molecular variance (AMOVA, <i>P</i> &lt; 0.001) indicated that the major genetic variation occurred within individuals (98%), while the degree of genetic differentiation between populations (2%) was relatively low. This study provides a theoretical basis for selecting and breeding new varieties with high-quality of monogerm in sugar beet and increasing the number of monogerm maintainer lines in sugar beet.</p>