Abstract Lagerstroemia spp. (crape myrtles) are popular woody ornamental flowering shrubs and trees distributed throughout temperate regions worldwide. In China, crape myrtles, especially the species L. indica , have been cultivated for nearly 1700 years, and germplasm resources are extensive. Therefore, investigating crape myrtle germplasm and their genetic diversity would assist international cultivar identification and breeding programs. Analysis of SSRs (Simple Sequence Repeats, also known as microsatellites) is currently the preferred method for the identification and determination of genetic relationships. The aim of this study was to develop and evaluate SSRs in crape myrtles as well as to evaluate genetic diversity and to perform fingerprinting analysis. Thirty-nine SSRs were isolated from enriched genomic libraries of L. indica . Primers were designed for 33 loci, 12 of which were polymorphic among 50 crape myrtle cultivars. In addition, we evaluated 14 SSRs from Lagerstroemia caudata . A total of 151 alleles were detected, and the average number of alleles per locus was 5.8. The observed heterozygosity ranged from 0.10 to 0.84, with a mean of 0.42 per locus. The average polymorphic information content (PIC) value and genetic similarity coefficient were 0.48 and 0.39, respectively, indicating wide genetic variation among all crape myrtle cultivars. Using the 26 SSRs above, all cultivars can be unambiguously identified and separated into two distinct groups. These newly developed SSRs can be efficiently used for crape myrtle genetic diversity assessment, DNA fingerprinting, and molecular breeding.