To clarify the genetic background of Tulipa iliensis, the genetic diversity was studied at the level of chloroplast genome. The cpDNA-PCR reaction system of T. iliensis was constructed by using the L16(45) orthogonal experiment design and single factor optimization screening experiment. The system was optimized by adjusting the Mg2+, dNTPs, primer concentration, Taq DNA polymerase, and template DNA concentration in the cpDNA-PCR reaction system. With the optimal system, primers were screened and performed cpDNA-PCR amplification to verify the stability of the reaction system, and the genetic diversity of the wild population of T. iliensis was also analyzed. The results showed that the optimal cpDNA-PCR reaction system for T. iliensis consisted of 2.00 mmol·L-1 Mg2+, 0.20 mmol·L-1 dNTPs, 0.40 μmol·L-1 primer concentration, 0.50 U Taq DNA polymerase, and 110 ng template DNA concentration. Using the optimal amplification system, 14 pairs of candidate primers (trnK-rps16, M3-M4, F71-R1516, trnD-trnE, psbB-psbH, trnL-trnF, atpB-rbcL, a1-b1, 1F-1R, rps8-rp116, atpI-atpH, accD-psaI, petG-trnP, 2F-2R) were selected from 16 pairs of candidate primer combinations for subsequent cpDNA-PCR amplification of T. iliensis. The established cpDNA-PCR reaction system for T. iliensis was stable in amplification and produced clear bands, genetic diversity analysis was performed on 54 T. iliensis individuals, The average length of amplified fragments using primer psbB-psbH was 582 bp, with 284 identified polymorphic sites, the nucleotide polymorphism Pi was 0.055, the average nucleotide difference number K was 30.261, and the gene flow (Nm=1.21>1) indicated that the genetic diversity of the T. iliensis population was high, and gene exchange among different populations was frequent. The cpDNA-PCR reaction system established in this study can be used to study the genetic diversity and population genetic structure of T. iliensis, providing a theoretical basis and technical support for the rational protection and sustainable utilization of wild tulip germplasm resources, and to provide a basis for scientific protection of T. iliensis germplasm resources.