Plant cultivars are important germplasm resources for socio-economic development. However, it is difficult to conduct accurate genetic evaluation on plant diversity solely on the basis of morphological traits which are easily affected by environmental conditions and may change during developmental stages of the plant. Developing DNA markers with high resolution and sensitivity, especially at cultivar level, is a global challenge. We report a good methodology for rapid and efficient detection of plant genetic diversity at cultivar level. A unique nucleotide molecular formula (NMF) was constructed for each crape myrtle using polymorphic nucleotide sites. Our results showed that the DNA sequence from chromatin remodeling gene region of the ubiquitin-proteasome system is useful for molecularly characterizing crape myrtle cultivars. This DNA marker technique will be of significant value for plant breeding, cultivar identification, protection of Plant Breeders’ rights and evaluation, protection and utilization of plant germplasm resources.