Acer pentaphyllum is rare and endangered plant endemic to Sichuan Province, China. This species is only distributed in the arid valley area of the upper and middle reaches of Yalong River. Exploring its genetic diversity characteristics can provide a theoretical basis for the protection and utilization of its genetic resources. In the paper, genetic diversity and genetic structure of 5 Acer pentaphyllum Diels populations from Sichuan (total about 44 individuals) were analyzed by ISSR (inter simple sequence repeat) markers. Eight highly stable and repeatable ISSR primers were used to detect a total of 38 loci, of which 35 were polymorphic sites (90.21% of the total). At the species level, the Shannon index (I) was 0.3924, Neis gene diversity index (He) was 0.2498, the coefficient of gene differentiation (Gst) was 0.3722, and the gene flow (Nm) was 0.8433. The software Popgen 32 analysis of the results showed that the genetic variation mainly existed in the population. At the population Level, I and He were 0.2125 and 0.1456, respectively. All of these results showed that Muli, Sanyagong and Kangdiing population had higher levels of genetic diversity, while Yajiang and Luomo had lower genetic diversity. The mantel analysis showed no significant correlation between genetic distance and geographic distance.
