The invention relates to a lagerstroemia indica dwarf plant type SNP molecular marker and application. Three lagerstroemia indica dwarf plant type SNP molecular markers M16337, M25207 and M38412 are developed by using an SLAF-seq technique, and the nucleotide sequences of the molecular markers are as shown in SEQ ID NO:1-3. The three molecular markers disclosed by the invention are adopted for assistant selective breeding, selection ahead of the seedling period can be achieved, the workload can be reduced, and thus the breeding process of lagerstroemia indica can be accelerated.