Lagerstroemia (crape myrtle) are famous ornamental plants with large pyramidal racemes, long flower duration, and diverse colors. However, little is known about the genetic structure and diversity of germplasm in Lagerstroemia. We genotyped 81 L. indica cultivars, five other species of Lagerstroemia, and 10 interspecific hybrids using 30 simple sequence repeat markers; 275 alleles were generated with a mean of nine alleles per locus. The mean polymorphism information content value, a measure of gene diversity, was 0.63, with a range from 0.25 to 0.86. The mean observed heterozygosity (0.51) tended to be lower than the mean expected heterozygosity (0.67). The mean F-statistics (F(ST), F(IS), and F(IT)) were 0.05, 0.20, and 0.24, respectively, indicating a high level of genetic variation among cultivars. Clustering analysis based on genetic distance divided the 96 genotypes into three distinct groups, which corresponded with their genetic backgrounds and geographic regions. L. indica cultivars and the other five L. species were grouped into different sub-clusters. Chinese and North American cultivars were divided into different clusters. These data about the genetic relationship among cultivars demonstrated the potential value of L. indica cultivars and other Lagerstroemia species for widening the genetic basis of breeding programs for this ornamental flower.