Idesia polycarpais Maxim. is an excellent woody oil tree species with significant economic and ecological value. Currently, the Inter-Retrotransposon Amplified Polymorphism (IRAP) marker system was developed in I. polycarpa based on the retrotransposon sequences of genome. Subsequently, 101 accessions from Guizhou Province were analyzed using 17 IRAP primers to construct molecular IDs and elucidate genetic relationships. The results indicated that the optimal 10-μL IRAP-PCR system was established as 0.6 μL template DNA, 1 μL IRAP primer, 6 μL PCR Mix, 2.4 μL ddH?O, and 40 PCR cycles via an L16(43) orthogonal test. Amplification with the 17 primers yielded 160 polymorphic fragments, averaging 9.4 per primer, with a polymorphic percentage of 100%. The average values of primers for the number of alleles (Na), effective number of alleles (Ne), Nei's gene diversity index (H), and Shannon's diversity index (I) were 2.000, 1.419, 0.261, and 0.412, respectively. Taking similarity coefficient 0.75 as a threshold, the 101 accessions were categorized into seven distinct groups. Furthermore, the germplasms, e.g. STZ74 andSTZ43 with the highest oil contents, were clustered into Group 6, and majority of those with the lowest oil contents were grouped into Group 1, e.g. STZ29, STZ41, STZ35, STZ30, and STZ31, et al. Seven core IRAP primers might efficiently differentiate all the accessions, thereby the obtained markers were used to construct DNA fingerprint and to generate molecular IDs. This study provides a valuable marker technology for the precise identification and genetic relationship analysis of I. polycarpa germplasms.